| Count | Error Message |
|---|
| 16 | Traceback (most recent call last):Show full stderrTraceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/Bio/File.py", line 72, in as_handle
with open(handleish, mode, **kwargs) as fp:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: expected str, bytes or os.PathLike object, not TextIOWrapper
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/jetstream2/scratch/main/jobs/72180231/tool_files/gbk2fa.py", line 58, in <module>
main()
File "/jetstream2/scratch/main/jobs/72180231/tool_files/gbk2fa.py", line 47, in main
for seq_record in SeqIO.parse(input_handle, 'genbank'):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/Bio/SeqIO/Interfaces.py", line 91, in __next__
return next(self.records)
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/Bio/GenBank/Scanner.py", line 512, in parse_records
record = self.parse(handle, do_features)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/Bio/GenBank/Scanner.py", line 495, in parse
if self.feed(handle, consumer, do_features):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/Bio/GenBank/Scanner.py", line 461, in feed
self._feed_first_line(consumer, self.line)
File "/usr/local/lib/python3.12/site-packages/Bio/GenBank/Scanner.py", line 1439, in _feed_first_line
raise ValueError(
ValueError: LOCUS line does not contain - at position 75 in date:
LOCUS JACULU010000010.1 115432 bp DNA linear 07-5月-2025 |
| 4 | /usr/local/lib/python3.12/site-packages/Bio/GenBank/Scanner.py:1525: BiopythonParserWarning: AttemShow full stderr/usr/local/lib/python3.12/site-packages/Bio/GenBank/Scanner.py:1525: BiopythonParserWarning: Attempting to parse malformed locus line:
'LOCUS 1-7 27714 bp RNA linear VRL 24-Nov-2023\n'
Found locus '1-7' size '27714' residue_type 'RNA'
Some fields may be wrong.
warnings.warn(
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72599727/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for '1-7-IBV'
00:00:00 Reading configuration file 'snpEff.config'. Genome: '1-7-IBV'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72599727/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome '1-7-IBV'
00:00:01 done
00:00:01 Chromosome: '1-7' length: 27714
java.lang.RuntimeException: Transcript 'Cytoplasmic.' is already in Gene 'Gene_525_20419'
at org.snpeff.interval.IntervalAndSubIntervals.add(IntervalAndSubIntervals.java:44)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.add(SnpEffPredictorFactory.java:145)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addMaturePeptide(SnpEffPredictorFactoryFeatures.java:164)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addFeatures(SnpEffPredictorFactoryFeatures.java:120)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:351)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
java.lang.RuntimeException: Error reading file '/jetstream2/scratch/main/jobs/72599727/working/snpeff_output/1-7-IBV/genes.gbk'
java.lang.RuntimeException: Transcript 'Cytoplasmic.' is already in Gene 'Gene_525_20419'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:365)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 2 | /usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it aShow full stderr/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '385..384' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '851..850' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '916..915' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1410..1409' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1419..1418' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1423..1422' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1424..1423' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1425..1424' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1428..1427' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1430..1429' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1432..1431' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '1785..1784' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '6544..6543' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '7488..7487' is a feature that spans the origin, but the sequence topology is undefined; setting feature location to None.
warnings.warn(
/usr/local/lib/python3.12/site-packages/Bio/GenBank/__init__.py:725: BiopythonParserWarning: it appears that '8003..8002' is a feature that spans the origin, |
| 2 | /usr/local/bin/snpEff: line 8: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-Show full stderr/usr/local/bin/snpEff: line 8: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72867002/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'snpeff_db'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'snpeff_db'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72867002/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-0/snpEff.config
00:00:00 done
Gpr.reader(544): java.util.zip.ZipException: Not in GZIP format
.
0 WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate.
java.lang.RuntimeException: FATAL ERROR: Most Exons do not have sequences!
. File '/jetstream2/scratch/main/jobs/72867002/working/snpeff_output/snpeff_db/genes.gtf' line 4859
'chromosome Pseudomonas Genome DB CDS 6537049 6537456 . - 0 gene_id "PGD1662774"; transcript_id "PGD1662774"; locus_tag "PA14_73420"; name "ribonuclease P"; replicon_xref "NC_008463.1";'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.error(SnpEffPredictorFactory.java:421)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactory.finishUp(SnpEffPredictorFactory.java:556)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:348)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
java.lang.RuntimeException: Error reading file '/jetstream2/scratch/main/jobs/72867002/working/snpeff_output/snpeff_db/genes.gtf'
java.lang.RuntimeException: FATAL ERROR: Most Exons do not have sequences!
. File '/jetstream2/scratch/main/jobs/72867002/working/snpeff_output/snpeff_db/genes.gtf' line 4859
'chromosome Pseudomonas Genome DB CDS 6537049 6537456 . - 0 gene_id "PGD1662774"; transcript_id "PGD1662774"; locus_tag "PA14_73420"; name "ribonuclease P"; replicon_xref "NC_008463.1";'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:353)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:369)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:02 Logging
00:00:03 Checking for updates...
00:00:04 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114748/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114748/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114748/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114748/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114748/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114748/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114748/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114749/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114749/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114749/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114749/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114749/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114749/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114749/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114750/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114750/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114750/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114750/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114750/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114750/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114750/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114751/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114751/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114751/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114751/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114751/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114751/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114751/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114752/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114752/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114752/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114752/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114752/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114752/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114752/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114753/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114753/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114753/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114753/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114753/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114753/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114753/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114754/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114754/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114754/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114754/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114754/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114754/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114754/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114755/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114755/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114755/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114755/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114755/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114755/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114755/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114756/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114756/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114756/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114756/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114756/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114756/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114756/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114757/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114757/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114757/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114757/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114757/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114757/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114757/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114758/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114758/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114758/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114758/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114758/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114758/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114758/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114759/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114759/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114759/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114759/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114759/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114759/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114759/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114760/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114760/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114760/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114760/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114760/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114760/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114760/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114761/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114761/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114761/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114761/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114761/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114761/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114761/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114762/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114762/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114762/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114762/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114762/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114762/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114762/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114763/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114763/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114763/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114763/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114763/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114763/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114763/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114764/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114764/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114764/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114764/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114764/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114764/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114764/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114765/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114765/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114765/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114765/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114765/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114765/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114765/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114766/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114766/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114766/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114766/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114766/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114766/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114766/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114767/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114767/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114767/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114767/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114767/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114767/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114767/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114768/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114768/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114768/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114768/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114768/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114768/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114768/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114769/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114769/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114769/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114769/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114769/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114769/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114769/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114770/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114770/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114770/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114770/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114770/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114770/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114770/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114771/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114771/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114771/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114771/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114771/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114771/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114771/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114772/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114772/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114772/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114772/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114772/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114772/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114772/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114773/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114773/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114773/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114773/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114773/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114773/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114773/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114774/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114774/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114774/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114774/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114774/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114774/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114774/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114775/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114775/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114775/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114775/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114775/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114775/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114775/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114776/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114776/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114776/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114776/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114776/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114776/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114776/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114777/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114777/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114777/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114777/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114777/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114777/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114777/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114778/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114778/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114778/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114778/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114778/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114778/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114778/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114779/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114779/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114779/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114779/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114779/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114779/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114779/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114780/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114780/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114780/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114780/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114780/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114780/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114780/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114781/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114781/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114781/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114781/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114781/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114781/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114781/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114782/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114782/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114782/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114782/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114782/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114782/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114782/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114783/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114783/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114783/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114783/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114783/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114783/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114783/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114784/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114784/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114784/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114784/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114784/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114784/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114784/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114785/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114785/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114785/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114785/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114785/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114785/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114785/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114786/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114786/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114786/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114786/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114786/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114786/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114786/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114787/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114787/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114787/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114787/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114787/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114787/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114787/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114788/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114788/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114788/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114788/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114788/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114788/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114788/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114789/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114789/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114789/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114789/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114789/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114789/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114789/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114790/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114790/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114790/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114790/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114790/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114790/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114790/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114791/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114791/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114791/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114791/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114791/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114791/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114791/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114792/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114792/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114792/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114792/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114792/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114792/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114792/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114793/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114793/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114793/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114793/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114793/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114793/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114793/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114794/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114794/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114794/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114794/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114794/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114794/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114794/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114795/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114795/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114795/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114795/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114795/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114795/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114795/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114796/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114796/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114796/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114796/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114796/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114796/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114796/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114797/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114797/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114797/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114797/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114797/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114797/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114797/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114798/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114798/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114798/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114798/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114798/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114798/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114798/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114799/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114799/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114799/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114799/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114799/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114799/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114799/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114800/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114800/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114800/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114800/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114800/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114800/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114800/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114801/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114801/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114801/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114801/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114801/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114801/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114801/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114802/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114802/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114802/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114802/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114802/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114802/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114802/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114803/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114803/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114803/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114803/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114803/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114803/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114803/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114804/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114804/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114804/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114804/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114804/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114804/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114804/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114805/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114805/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114805/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114805/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114805/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114805/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114805/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114806/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114806/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114806/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114806/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114806/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114806/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114806/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114807/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114807/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114807/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114807/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114807/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114807/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114807/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114808/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114808/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114808/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114808/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114808/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114808/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114808/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114809/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114809/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114809/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114809/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114809/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114809/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114809/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114810/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114810/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114810/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114810/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114810/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114810/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114810/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114811/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114811/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114811/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114811/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114811/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114811/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114811/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114812/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114812/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114812/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114812/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114812/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114812/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114812/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114813/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114813/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114813/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114813/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114813/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114813/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114813/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114814/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114814/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114814/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114814/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114814/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114814/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114814/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114815/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114815/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114815/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114815/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114815/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114815/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114815/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114816/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114816/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114816/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114816/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114816/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114816/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114816/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114817/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114817/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114817/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114817/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114817/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114817/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114817/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114818/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114818/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114818/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114818/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114818/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114818/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114818/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114819/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114819/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114819/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114819/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114819/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114819/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114819/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114820/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114820/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114820/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114820/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114820/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114820/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114820/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114821/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114821/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114821/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114821/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114821/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114821/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114821/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114822/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114822/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114822/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114822/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114822/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114822/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114822/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114823/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114823/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114823/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114823/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114823/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114823/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114823/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114824/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114824/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114824/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114824/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114824/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114824/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114824/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114825/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114825/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114825/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114825/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114825/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114825/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114825/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114826/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114826/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114826/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114826/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114826/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114826/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114826/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114827/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114827/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114827/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114827/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114827/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114827/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114827/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114828/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114828/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114828/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114828/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114828/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114828/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114828/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114829/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114829/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114829/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114829/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114829/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114829/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114829/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114830/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114830/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114830/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114830/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114830/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114830/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114830/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114831/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114831/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114831/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114831/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114831/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114831/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114831/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114832/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114832/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114832/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114832/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114832/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114832/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114832/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114833/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114833/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114833/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114833/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114833/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114833/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114833/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114834/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114834/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114834/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114834/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114834/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114834/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114834/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114835/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114835/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114835/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114835/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114835/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114835/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114835/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114836/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114836/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114836/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114836/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114836/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114836/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114836/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114837/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114837/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114837/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114837/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114837/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114837/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114837/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114838/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114838/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114838/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114838/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114838/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114838/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114838/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114839/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114839/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114839/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114839/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114839/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114839/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114839/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114840/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114840/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114840/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114840/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114840/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114840/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114840/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114841/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114841/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114841/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114841/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114841/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114841/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114841/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114844/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114844/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114844/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114844/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114844/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114844/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114844/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114845/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114845/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114845/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114845/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114845/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114845/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114845/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114846/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72114846/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aerugonisa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aerugonisa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72114846/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aerugonisa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72114846/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72114846/working/snpeff_output/Pseudomonas_aerugonisa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72114846/working/snpeff_output/genomes/Pseudomonas_aerugonisa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72114846/working/snpeff_output/Pseudomonas_aerugonisa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/120/72120800/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/120/72120800/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'BBCMM1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132672/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132672/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132672/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132672/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132672/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132672/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132672/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132673/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132673/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132673/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132673/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132673/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132673/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132673/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132674/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132674/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132674/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132674/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132674/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132674/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132674/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132675/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132675/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132675/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132675/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132675/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132675/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132675/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132676/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132676/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132676/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132676/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132676/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132676/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132676/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132677/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132677/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132677/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132677/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132677/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132677/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132677/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132678/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132678/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132678/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132678/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132678/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132678/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132678/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132679/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132679/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132679/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132679/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132679/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132679/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132679/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132680/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132680/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132680/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132680/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132680/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132680/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132680/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132681/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132681/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132681/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132681/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132681/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132681/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132681/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132682/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132682/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132682/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132682/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132682/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132682/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132682/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132683/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132683/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132683/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132683/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132683/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132683/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132683/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132684/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132684/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132684/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132684/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132684/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132684/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132684/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132685/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132685/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132685/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132685/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132685/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132685/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132685/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132686/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132686/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132686/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132686/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132686/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132686/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132686/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132687/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132687/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132687/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132687/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132687/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:02 Total: 0 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Reading sequences :
00:00:02 FASTA file: '/jetstream2/scratch/main/jobs/72132687/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:02 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132687/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:02 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132688/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132688/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132688/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132688/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132688/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132688/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132688/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132689/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132689/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132689/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132689/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132689/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132689/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132689/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132690/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132690/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132690/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132690/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132690/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132690/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132690/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132691/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132691/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132691/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132691/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132691/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132691/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132691/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132692/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132692/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132692/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132692/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132692/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132692/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132692/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132693/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132693/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132693/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132693/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132693/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132693/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132693/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132694/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132694/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132694/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132694/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132694/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132694/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132694/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132695/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132695/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132695/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132695/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132695/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132695/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132695/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132696/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132696/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132696/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132696/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132696/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132696/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132696/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132697/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132697/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132697/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132697/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132697/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132697/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132697/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132698/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132698/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132698/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132698/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132698/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132698/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132698/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132699/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132699/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132699/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132699/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132699/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132699/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132699/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132700/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132700/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132700/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132700/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132700/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132700/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132700/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132701/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132701/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132701/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132701/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132701/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:02 Total: 0 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Reading sequences :
00:00:02 FASTA file: '/jetstream2/scratch/main/jobs/72132701/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:02 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132701/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:02 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132702/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132702/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132702/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132702/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132702/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132702/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132702/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132703/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132703/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132703/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132703/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132703/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132703/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132703/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132704/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132704/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132704/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132704/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132704/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132704/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132704/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132705/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132705/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132705/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132705/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132705/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132705/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132705/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132706/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132706/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132706/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132706/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132706/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132706/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132706/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132707/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132707/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132707/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132707/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132707/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132707/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132707/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132708/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132708/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132708/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132708/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132708/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132708/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132708/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132709/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132709/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132709/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132709/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132709/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132709/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132709/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132710/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132710/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132710/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132710/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132710/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132710/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132710/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132711/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132711/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132711/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132711/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132711/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132711/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132711/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132712/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132712/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132712/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132712/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132712/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132712/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132712/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132713/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132713/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132713/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132713/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132713/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132713/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132713/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132714/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132714/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132714/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132714/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132714/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132714/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132714/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132715/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132715/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132715/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132715/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132715/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132715/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132715/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132716/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132716/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132716/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132716/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132716/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132716/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132716/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132717/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132717/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132717/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132717/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132717/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:02 Total: 0 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Reading sequences :
00:00:02 FASTA file: '/jetstream2/scratch/main/jobs/72132717/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:02 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132717/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:02 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132718/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132718/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132718/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132718/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132718/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132718/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132718/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132719/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132719/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132719/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132719/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132719/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132719/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132719/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132720/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132720/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132720/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132720/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132720/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132720/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132720/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132721/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132721/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132721/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132721/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132721/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132721/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132721/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132722/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132722/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132722/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132722/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132722/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132722/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132722/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132723/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132723/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132723/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132723/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132723/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132723/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132723/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132724/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132724/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132724/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132724/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132724/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132724/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132724/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132725/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132725/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132725/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132725/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132725/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132725/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132725/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132726/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132726/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132726/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132726/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132726/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132726/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132726/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132727/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132727/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132727/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132727/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132727/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132727/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132727/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:02 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132728/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132728/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132728/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132728/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132728/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132728/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132728/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132729/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132729/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132729/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132729/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132729/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132729/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132729/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132730/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132730/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132730/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132730/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132730/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132730/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132730/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132731/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132731/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132731/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132731/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132731/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132731/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132731/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132732/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132732/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132732/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132732/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132732/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132732/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132732/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132733/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132733/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132733/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132733/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132733/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132733/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132733/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132734/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132734/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132734/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132734/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132734/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132734/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132734/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132735/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132735/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132735/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132735/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132735/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132735/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132735/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132736/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132736/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132736/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132736/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132736/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132736/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132736/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132737/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132737/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132737/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132737/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132737/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132737/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132737/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132738/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132738/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132738/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132738/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132738/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132738/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132738/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:02 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132739/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132739/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132739/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132739/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132739/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132739/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132739/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132740/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132740/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132740/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132740/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132740/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132740/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132740/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132741/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132741/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132741/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132741/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132741/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132741/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132741/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132742/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132742/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132742/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132742/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132742/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132742/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132742/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132743/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132743/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132743/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132743/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132743/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132743/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132743/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132744/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132744/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132744/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132744/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132744/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132744/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132744/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132745/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132745/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132745/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132745/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132745/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132745/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132745/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132746/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132746/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132746/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132746/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132746/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132746/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132746/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132747/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132747/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132747/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132747/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132747/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132747/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132747/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132748/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132748/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132748/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132748/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132748/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132748/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132748/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132749/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132749/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132749/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132749/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132749/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132749/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132749/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132750/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132750/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132750/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132750/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132750/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132750/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132750/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132751/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132751/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132751/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132751/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132751/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132751/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132751/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132752/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132752/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132752/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132752/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132752/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132752/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132752/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132753/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132753/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132753/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132753/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132753/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132753/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132753/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132754/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132754/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132754/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132754/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132754/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132754/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132754/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132755/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132755/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132755/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132755/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132755/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132755/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132755/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132756/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132756/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132756/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132756/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132756/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:02 Total: 0 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Reading sequences :
00:00:02 FASTA file: '/jetstream2/scratch/main/jobs/72132756/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:02 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132756/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:02 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132757/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132757/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132757/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132757/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132757/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132757/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132757/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132758/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132758/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132758/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132758/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132758/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132758/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132758/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132759/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132759/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132759/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132759/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132759/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132759/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132759/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132760/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132760/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132760/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132760/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132760/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132760/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132760/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132761/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132761/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132761/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132761/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132761/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132761/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132761/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132762/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132762/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132762/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132762/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132762/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132762/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132762/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132763/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132763/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132763/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132763/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132763/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132763/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132763/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132764/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132764/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132764/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132764/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132764/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132764/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132764/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132765/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132765/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132765/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132765/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132765/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132765/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132765/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132766/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132766/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132766/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132766/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132766/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132766/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132766/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132767/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132767/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132767/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132767/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132767/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132767/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132767/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132768/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132768/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132768/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132768/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132768/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132769/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132769/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132769/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132769/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132769/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132769/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132769/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132770/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132770/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132770/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132770/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132770/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132770/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132770/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132771/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132771/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132771/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132771/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132771/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132771/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132771/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132772/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132772/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132772/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132772/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132772/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132772/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132772/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132773/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132773/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132773/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132773/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132773/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132773/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132773/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132774/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132774/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132774/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132774/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132774/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132774/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132774/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132775/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132775/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132775/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132775/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132775/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132775/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132775/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132776/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132776/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132776/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132776/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132776/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132776/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132776/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132777/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132777/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132777/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132777/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132777/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132777/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132777/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132778/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132778/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132778/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132778/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132778/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132778/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132778/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132779/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132779/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132779/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132779/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132779/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132779/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132779/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132780/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132780/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132780/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132780/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132780/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132780/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132780/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132781/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132781/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132781/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132781/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132781/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132781/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132781/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132782/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132782/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132782/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132782/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132782/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132782/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132782/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132783/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132783/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132783/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132783/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132783/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132783/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132783/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132784/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72132784/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72132784/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72132784/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72132784/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72132784/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72132784/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72135131/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72135131/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72135131/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72135131/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72135131/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72135131/working/snpeff_output/genomes/Pseudomonasaeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72135131/working/snpeff_output/Pseudomonasaeruginosa/sequences.fa'
00:00:01 Reading sequence 'ABFUBW010000001.1', length: 368936
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000002.1', length: 350374
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000003.1', length: 344305
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000004.1', length: 308086
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000005.1', length: 256389
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000006.1', length: 226942
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000007.1', length: 226325
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000008.1', length: 219277
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFUBW010000009.1', length: 217899
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ABFU |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/145/72145795/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/145/72145795/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147308/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147308/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147308/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147308/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147308/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147308/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147308/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147309/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147309/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147309/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147309/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147309/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147309/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147309/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147310/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147310/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147310/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147310/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147310/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147310/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147310/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147311/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147311/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147311/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147311/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147311/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147311/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147311/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147312/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147312/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147312/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147312/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147312/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147312/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147312/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147313/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147313/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147313/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147313/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147313/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147313/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147313/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147314/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147314/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147314/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147314/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147314/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147314/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147314/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147315/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147315/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147315/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147315/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147315/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147315/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147315/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147316/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147316/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147316/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147316/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147316/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147316/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147316/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147317/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147317/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147317/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147317/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147317/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147317/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147317/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147318/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147318/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147318/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147318/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147318/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147318/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147318/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147319/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147319/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147319/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147319/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147319/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147319/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147319/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147320/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147320/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147320/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147320/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147320/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147320/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147320/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147321/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147321/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147321/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147321/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147321/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147321/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147321/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147322/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147322/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147322/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147322/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147322/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147322/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147322/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147323/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147323/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147323/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147323/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147323/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147323/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147323/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147324/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147324/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147324/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147324/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147324/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147324/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147324/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147325/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147325/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147325/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147325/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147325/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147325/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147325/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147326/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147326/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147326/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147326/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147326/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147326/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147326/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147327/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147327/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147327/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147327/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147327/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147327/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147327/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147328/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147328/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147328/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147328/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147328/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147328/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147328/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147329/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147329/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147329/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147329/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147329/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147329/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147329/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147330/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147330/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147330/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147330/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147330/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147330/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147330/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147331/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147331/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147331/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147331/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147331/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147331/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147331/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147332/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147332/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147332/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147332/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147332/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147332/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147332/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147333/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147333/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147333/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147333/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147333/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147333/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147333/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147334/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147334/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147334/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147334/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147334/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147334/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147334/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147335/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147335/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147335/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147335/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147335/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147335/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147335/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147336/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147336/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147336/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147336/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147336/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147336/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147336/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147337/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147337/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147337/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147337/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147337/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147337/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147337/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147338/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147338/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147338/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147338/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147338/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147338/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147338/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147339/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147339/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147339/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147339/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147339/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147339/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147339/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147340/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147340/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147340/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147340/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147340/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147340/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147340/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147341/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147341/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147341/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147341/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147341/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147341/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147341/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147342/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147342/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147342/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147342/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147342/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147342/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147342/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147343/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147343/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147343/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147343/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147343/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147343/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147343/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147344/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147344/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147344/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147344/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147344/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147344/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147344/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147345/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147345/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147345/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147345/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147345/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147345/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147345/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147346/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147346/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147346/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147346/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147346/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147346/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147346/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147347/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147347/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147347/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147347/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147347/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147347/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147347/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147348/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147348/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147348/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147348/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147348/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147348/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147348/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147349/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147349/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147349/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147349/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147349/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147349/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147349/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147350/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147350/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147350/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147350/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147350/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147350/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147350/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147351/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147351/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147351/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147351/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147351/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147351/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147351/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147352/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147352/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147352/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147352/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147352/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147352/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147352/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147353/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147353/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147353/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147353/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147353/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147353/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147353/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147354/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147354/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147354/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147354/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147354/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147354/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147354/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147355/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147355/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147355/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147355/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147355/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147355/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147355/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147356/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147356/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147356/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147356/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147356/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147356/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147356/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147357/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147357/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147357/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147357/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147357/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147357/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147357/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147358/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147358/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147358/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147358/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147358/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147358/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147358/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147359/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147359/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147359/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147359/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147359/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147359/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147359/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147360/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147360/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147360/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147360/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147360/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147360/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147360/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147361/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147361/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147361/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147361/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147361/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147361/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147361/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147362/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147362/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147362/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147362/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147362/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147362/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147362/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147363/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147363/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147363/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147363/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147363/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147363/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147363/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147364/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147364/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147364/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147364/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147364/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147364/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147364/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147365/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147365/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147365/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147365/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147365/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147365/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147365/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147366/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147366/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147366/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147366/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147366/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147366/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147366/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147367/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147367/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147367/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147367/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147367/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147367/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147367/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147368/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147368/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147368/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147368/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147368/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147368/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147368/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147369/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147369/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147369/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147369/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147369/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147369/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147369/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147370/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147370/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147370/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147370/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147370/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147370/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147370/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147371/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147371/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147371/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147371/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147371/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147371/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147371/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147372/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147372/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147372/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147372/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147372/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147372/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147372/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147373/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147373/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147373/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147373/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147373/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147373/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147373/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147374/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147374/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147374/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147374/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147374/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147374/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147374/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147375/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147375/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147375/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147375/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147375/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147375/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147375/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147376/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147376/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147376/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147376/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147376/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147376/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147376/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147377/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147377/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147377/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147377/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147377/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147377/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147377/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147378/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147378/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147378/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147378/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147378/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147378/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147378/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147379/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147379/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147379/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147379/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147379/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147379/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147379/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147380/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147380/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147380/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147380/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147380/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147380/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147380/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147381/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147381/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147381/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147381/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147381/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147381/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147381/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147382/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147382/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147382/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147382/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147382/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147382/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147382/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147383/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147383/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147383/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147383/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147383/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147383/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147383/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147384/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147384/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147384/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147384/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147384/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147384/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147384/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147385/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147385/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147385/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147385/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147385/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147385/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147385/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147386/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147386/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147386/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147386/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147386/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147386/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147386/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147387/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147387/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147387/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147387/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147387/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147387/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147387/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147388/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147388/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147388/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147388/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147388/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147388/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147388/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147389/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147389/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147389/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147389/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147389/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147389/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147389/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147390/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147390/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147390/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147390/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147390/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147390/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147390/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147391/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147391/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147391/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147391/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147391/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147391/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147391/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147392/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147392/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147392/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147392/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147392/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147392/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147392/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147393/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147393/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147393/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147393/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147393/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147393/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147393/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147394/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147394/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147394/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147394/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147394/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147394/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147394/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147395/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147395/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147395/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147395/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147395/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147395/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147395/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147396/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147396/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147396/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147396/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147396/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147396/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147396/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147397/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147397/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147397/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147397/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147397/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147397/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147397/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147398/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147398/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147398/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147398/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147398/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147398/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147398/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147399/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147399/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147399/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147399/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147399/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147399/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147399/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147400/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147400/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147400/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147400/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147400/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147400/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147400/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147401/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147401/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147401/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147401/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147401/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147401/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147401/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147402/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147402/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147402/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147402/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147402/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147402/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147402/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147403/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147403/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147403/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147403/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147403/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147403/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147403/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147404/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147404/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147404/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147404/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147404/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147404/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147404/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147405/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147405/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147405/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147405/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147405/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147405/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147405/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147406/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147406/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147406/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147406/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147406/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147406/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147406/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147407/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72147407/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'P_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'P_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72147407/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'P_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72147407/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72147407/working/snpeff_output/P_aeruginosa/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72147407/working/snpeff_output/genomes/P_aeruginosa.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72147407/working/snpeff_output/P_aeruginosa/sequences.fa'
00:00:01 Reading sequence 'accn|NC_002516', length: 6264404
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'accn|NC_002516' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/152/72152788/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/152/72152788/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh37'
00:00:00 Reading config file: /corral4/main/jobs/072/152/72152788/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153195/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153195/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153195/inputs/dataset_d95bc63b-664e-434d-b624-651aa6086d69.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153196/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153196/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/f/0/dataset_df094e4d-2e23-4efa-8827-2c4502631cd6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153197/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153197/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/0/1/dataset_a010f1a7-cd22-441e-8caa-5475bc975b1f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153198/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153198/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153198/inputs/dataset_cd6f0597-9714-4034-9363-e77c2700942c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153199/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153199/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/9/c/dataset_79c5b693-efd9-45de-9e4d-0bf6a4f8e5d0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153200/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153200/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/3/2/dataset_032cdd87-6977-4f0e-be0f-487d3a697f28.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153201/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153201/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153201/inputs/dataset_25bc3faf-bc0a-4303-9cee-0ca4740c8581.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153202/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153202/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/9/5/dataset_a95c6115-1078-46d9-b47b-2d1bad986705.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153203/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153203/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/b/9/dataset_2b9afd15-9459-462e-b1c9-b87e48ed12b4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153204/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153204/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/a/dataset_b1a15c3a-d9f2-4dab-bc97-2be24e862454.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153205/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153205/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153205/inputs/dataset_5d30e132-4994-47a1-9418-8584c777d000.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153206/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153206/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/3/4/dataset_c342e438-8117-4038-b719-585a78e2fc9d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153207/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153207/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153207/inputs/dataset_b68dd060-568a-489c-93ad-40769f1a2c51.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153208/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153208/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/0/7/dataset_6079ccbe-52ae-40db-b425-8e426d5a9b07.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153209/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153209/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/d/9/dataset_bd91e2a4-2fd9-4ce2-802c-138d93f00e1b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153210/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153210/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153210/inputs/dataset_bb7e479c-2f29-43bc-a3a4-5d9ffb9df839.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153211/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153211/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/0/2/dataset_e025028e-9ca7-4bf7-a946-f44cc9601861.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153212/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153212/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/2/5/dataset_525679d2-8c3f-44cd-baf5-f82c09cbedf8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153213/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153213/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153213/inputs/dataset_682ec1fa-3ff8-47c8-a931-fb3a4bc1f13a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153214/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153214/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/2/9/dataset_0298aa6a-979f-4704-8e4d-aff9df4c7f24.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153215/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153215/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153215/inputs/dataset_a55f0881-395e-4488-a9d9-712b6df50a9f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153216/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153216/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153216/inputs/dataset_bff3dd72-ec63-455f-904a-24b102f33a10.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153217/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153217/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153217/inputs/dataset_7314aabd-c838-4249-950d-a57368968dcf.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153218/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153218/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/f/d/dataset_6fd8baf7-6906-4b4d-bdbd-fdae75c0881b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153219/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153219/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153219/inputs/dataset_980f32e1-c81f-4df9-b7c6-d397273e2d09.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153220/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153220/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/0/0/dataset_000f0226-745a-472f-940c-452a5886f0f0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153221/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153221/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/8/d/dataset_28d32649-6437-4870-a3c2-e253bafbce47.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153222/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153222/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153222/inputs/dataset_df43efdd-f67a-4648-bc2a-c3c37c4f554e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153223/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153223/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/5/dataset_435680d3-035b-417c-b93e-f172799647fb.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153224/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153224/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/0/0/dataset_100c9fc4-fb66-4fad-bb38-f4be4bf0f1d8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153225/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153225/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/3/e/dataset_83e7e872-1536-47ae-a183-382d67855335.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153226/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153226/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/2/7/dataset_3274ba1f-1c55-4818-a543-8d4314d02aee.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153227/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153227/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153227/inputs/dataset_748e529f-2e0e-4675-be53-4809bc78ede6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153228/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153228/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/d/d/dataset_6dd95ea3-95ba-4368-b88f-da48f4636975.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153229/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153229/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153229/inputs/dataset_68470bd7-1577-460e-84f6-4c98475fd3a0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153230/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153230/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/0/3/dataset_203c279f-c434-4f98-afb5-e43aebc24fb5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153231/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153231/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/1/8/dataset_618a811d-e41f-4f17-923a-a9a56cdbd115.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153232/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153232/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/3/f/dataset_13fcc053-4e4d-4ac6-a756-1c4d9dc8e636.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153233/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153233/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153233/inputs/dataset_6f6d3c67-84cf-4890-9285-e13ea3f77ad3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153234/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153234/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/9/c/dataset_39cdbddf-1973-4244-b4dd-2e1ee9445ca8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153235/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153235/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153235/inputs/dataset_0f5044da-5395-4448-b7eb-ee638fb3ce04.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153236/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153236/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153236/inputs/dataset_ed3c9656-10c7-4fce-9bf7-8545e64d0667.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153237/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153237/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153237/inputs/dataset_f56b6194-0ade-4eab-874b-e66051251e2e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153238/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153238/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153238/inputs/dataset_df7516fe-4bd9-41dd-a1f3-2060fe9250d0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153239/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153239/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/f/3/dataset_6f3bfc62-cee5-4179-ba35-255e7799acea.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153240/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153240/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/0/5/dataset_805b8071-d1e5-4ac1-b7c4-763331ecaea6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153241/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153241/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153241/inputs/dataset_9b9c6457-20b2-4f1b-b734-8ce1759fe6b5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153242/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153242/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/4/d/dataset_34d06fa1-c2b8-4ded-a4cb-1fe92dd86d83.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153243/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153243/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153243/inputs/dataset_a94dccac-0300-465b-ae65-0a654178dea0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153244/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153244/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/8/3/dataset_d831f973-52e4-48fc-a601-8cb37e5abed3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153245/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153245/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/b/7/dataset_6b70a991-3675-45c0-be5c-e80ef05a0a01.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153246/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153246/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/6/d/dataset_16d548dc-8592-4b4b-85ab-ef360f288692.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153247/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153247/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/6/a/dataset_36af28e6-0518-4957-9c08-3f394f994c20.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153248/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153248/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/9/e/dataset_69e4442c-ef18-44d1-9157-ece70535283d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153249/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153249/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153249/inputs/dataset_080bc15e-8925-473e-9724-aec9006189bc.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153250/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153250/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/c/c/dataset_fcc33685-3cec-41b9-870d-241cc281ebaa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153251/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153251/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/e/a/dataset_bea42387-35c3-4a63-9f2f-5e81aa7e9bd1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153252/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153252/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/0/5/dataset_305bab1b-1a38-48a9-9a9f-512da3c289af.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153253/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153253/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/0/e/dataset_c0e723d2-0882-4da8-b278-8fcacd073539.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153254/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153254/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153254/inputs/dataset_9617a65c-400b-4f5c-ac52-19e22eb30721.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153255/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153255/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153255/inputs/dataset_196b5699-ed25-44bd-84eb-b063ceb4259e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153256/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153256/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153256/inputs/dataset_ad780b1d-af86-4f9a-93fa-e878be00885a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153257/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153257/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153257/inputs/dataset_cd7c6b46-70b4-467a-8851-06b479cb9814.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153258/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153258/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153258/inputs/dataset_f3f15bd9-c8be-4102-afa3-5e48b5c29366.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153259/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153259/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/0/3/dataset_703cb53e-6e81-43dd-8fed-787e549af33c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153260/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153260/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/a/a/dataset_2aab484e-b4b9-49c6-97f3-ce2bb7ae5eda.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153261/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153261/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/b/1/dataset_6b186dc6-95eb-436a-9fff-7a2dcda25ab4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153262/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153262/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/f/1/dataset_0f16da8a-2a10-4ce4-b673-625c9e77f72b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153263/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153263/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/9/4/dataset_e9458c2d-51bd-4ae3-beda-f17ff35d82b1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153264/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153264/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/a/3/dataset_fa36a54c-b45f-4c76-9401-539917e58851.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153265/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153265/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/7/dataset_b17eb3c2-7f36-42be-b19b-732f2d5e5727.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153266/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153266/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153266/inputs/dataset_136da2e3-836c-4630-ad71-96f95e304d1c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153267/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153267/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/2/9/dataset_929fa0e8-eee4-45ff-99e6-eaf707e18bab.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153268/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153268/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153268/inputs/dataset_72fa2777-4641-4ab9-b516-b696df1c4236.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153269/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153269/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/a/f/dataset_0aff25a5-2964-4cdd-84e6-d0b0c400a6a8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153270/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153270/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/e/7/dataset_ce7ac756-4dc7-44e0-be41-ef711be9501a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153271/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153271/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/2/1/dataset_b21c9ebe-2a08-4cca-a3c6-b8e93a17a398.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153272/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153272/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/e/d/dataset_fed0bace-c05a-4615-a5a2-42b3d0a12f35.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153273/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153273/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/4/d/dataset_e4d24101-f420-4c61-b1e8-6d53cf60e538.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153274/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153274/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/3/d/dataset_a3d0b904-4340-4a56-a3ba-0a7a3b083b0b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153275/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153275/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/8/d/dataset_b8d00513-d19f-4e58-8d8b-a75f56c96835.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153276/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153276/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/8/2/dataset_b82a960d-5048-486e-b590-22670ab66fb0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153277/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153277/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/7/d/dataset_47d6504a-b329-44fc-8bfb-562155a66280.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153278/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153278/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/e/3/dataset_de3ff80c-68e8-450e-b8e5-bd7e47341fa8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153279/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153279/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/0/5/dataset_e05df72a-a702-4ff1-993e-1cddcb73d83f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153280/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153280/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153280/inputs/dataset_c44e7f63-3e0a-4ede-a0f1-7592edbec187.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153281/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153281/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153281/inputs/dataset_d3837626-f485-4cab-9f84-6254fce47169.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153282/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153282/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/1/1/dataset_911b24a0-6c86-42b4-b682-72d9566f45ea.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153283/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153283/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/2/d/dataset_72d58135-e64e-453e-9cd0-14bb18d46405.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153284/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153284/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/a/5/dataset_fa5bb06b-ec8c-4978-b920-0f3cd515d25e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153285/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153285/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/4/5/dataset_b45f97fd-e9b0-486e-a4d7-5031847de6c6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153286/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153286/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/7/0/dataset_170b312a-7e91-4af3-9d74-40fe0b5626d7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153287/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153287/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/f/1/dataset_7f1699a0-665d-4381-a019-fda6a2b57660.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153288/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153288/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/0/e/dataset_20ecb23f-22bf-49ee-8781-b05f6afe3254.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153289/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153289/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/8/4/dataset_484775d8-04c9-4a2b-bd15-a164d96ff166.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153290/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153290/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/c/a/dataset_3cadf0c0-d87d-4793-843e-abe92364b4b2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153291/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153291/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153291/inputs/dataset_b54990a3-b01f-48bb-a411-914d1beb503d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153292/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153292/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/5/b/dataset_55b1f1bd-95b9-4f76-9af8-21779da3fea3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153293/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153293/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153293/inputs/dataset_09ee83c0-0eb9-42e3-8361-41a43cc1fd09.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153294/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153294/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/4/d/dataset_74d26f0c-83ea-458f-99a1-f1acfd3126fe.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153295/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153295/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153295/inputs/dataset_39871360-579f-4b86-b09f-c26c6911dce6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153296/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153296/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/2/0/dataset_0203aa02-98d8-484a-866e-2d63c31f5bf0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153297/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153297/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/5/0/dataset_e50c355d-80f1-421e-8755-f8b06cb067a3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153298/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153298/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/3/a/dataset_f3a91be2-1251-48b8-ab45-e8de9fd5aeca.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153299/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153299/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/2/b/dataset_92b82171-2f79-471e-b821-e51c0839e4ba.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153300/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153300/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/2/e/dataset_92e8dce9-1ea3-4199-91fd-ea947d483c65.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153301/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153301/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/f/d/dataset_bfd22c3b-21df-4aef-bafe-d873f412b493.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153302/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153302/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/0/6/dataset_40669698-2e79-410d-9799-fbf4c87d9000.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153303/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153303/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/0/f/dataset_30f25e71-dc28-4f24-a849-bfc760d691b7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153304/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153304/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/e/1/dataset_ce114631-f989-4439-9f35-65c25f299047.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153305/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153305/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/9/d/dataset_79d41f5a-8bd2-42d4-8bfa-259246913175.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153306/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153306/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/8/8/dataset_588e3fe1-fb14-49dd-a081-9ed57a98629d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153307/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153307/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/b/7/dataset_8b773848-6ba2-4176-b8be-b64d4ac9ff9c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153308/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153308/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/0/1/dataset_a01e64ca-9b01-4c23-82ac-982bbdbf1fd1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153309/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153309/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/8/6/dataset_a86b81ba-4c6a-40c1-b5c2-2c73e0c70162.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153310/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153310/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/5/3/dataset_253bd1f8-e0a4-411d-8604-59236db1d362.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153311/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153311/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153311/inputs/dataset_8e5fd47d-a2a5-4363-b5de-96345aefbd6e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153312/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153312/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/9/8/dataset_9989e108-702f-41ad-a79e-fa4b800df59f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153313/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153313/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/3/dataset_433b8f1d-3aea-4250-a463-984641f1eca8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153314/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153314/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/2/1/dataset_b210a752-144c-452e-a142-1def770f9b0c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153315/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153315/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/e/1/dataset_6e191760-d84c-4901-b98c-f7616129ccde.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153316/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153316/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/b/2/dataset_4b2fe6fd-3164-4196-b0a7-866de4459649.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153317/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153317/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/0/f/dataset_20f7f57c-eb37-49e8-a44e-f77636fa6ef7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153318/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153318/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153318/inputs/dataset_7b3b984e-d3ef-4e43-a9c5-a25341f0f82c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153319/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153319/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153319/inputs/dataset_9aebdca8-c723-410f-a753-2d371b652718.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153320/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153320/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/6/4/dataset_a64d47b6-f625-4e4b-98d2-adce48d0854d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153321/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153321/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/4/7/dataset_9476225d-5e1d-4d6b-a1bd-3460f92d46ad.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153322/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153322/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/0/9/dataset_609f4722-a888-4edf-a41c-596a4867e775.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153323/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153323/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/c/e/dataset_bce3e5b0-4b67-43e6-b842-fe7532a6b08a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153324/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153324/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/b/8/dataset_eb833405-50d8-4dd5-8994-abb9bb68d2a3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153325/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153325/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/f/dataset_43f4f717-a60f-47cb-a469-0f506b767741.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153326/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153326/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153326/inputs/dataset_55758889-b6b7-4116-9889-0ee904de7852.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153327/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153327/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/9/3/dataset_e93b9985-39ba-4b11-a4c8-822ff396a2c4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153328/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153328/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/2/b/dataset_52b11c96-5359-48d3-bd2d-931265337dc9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153329/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153329/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/1/d/dataset_61d432db-b5f7-48a0-82ed-17eda6f45f56.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153330/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153330/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153330/inputs/dataset_9009e613-f3e1-4232-a6df-f63fe20e4b86.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153331/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153331/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153331/inputs/dataset_879fc460-1902-425f-9789-657a0132d9ee.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153332/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153332/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153332/inputs/dataset_ab6c9f8a-114b-4b0a-acfa-88e428cf3b18.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153333/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153333/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153333/inputs/dataset_f695bddb-13d7-4334-a0b7-14b92393a800.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153334/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153334/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/b/2/dataset_3b28d707-46dd-42e1-a890-a876f624ea01.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153335/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153335/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/1/6/dataset_516f8704-c155-4e1d-86cf-9cb1fa83590b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153336/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153336/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/8/8/dataset_e88f14fc-f2e9-4510-b494-8e08abce3560.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153337/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153337/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/6/7/dataset_06797006-7a2b-481f-8bd3-17661136374d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153338/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153338/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/d/3/dataset_2d3368b5-58f0-4df5-91ae-cf94ff2af66a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153339/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153339/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/6/c/dataset_16cafcf3-11d4-4a05-8889-f101903f434d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153340/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153340/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/7/2/dataset_87228687-a3f9-4e58-a00e-2a9aec8661a3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153341/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153341/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/7/d/dataset_a7d16002-5e34-48e6-addd-a4549e287893.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153342/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153342/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153342/inputs/dataset_d06010ea-756d-4529-ae30-7eda57090e1a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153343/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153343/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/9/a/dataset_e9afad24-6b42-4f29-a0b2-f1af3226e9aa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153344/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153344/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153344/inputs/dataset_ba06ebb7-40da-4560-9128-07dc8b281c64.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153345/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153345/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/7/1/dataset_571a87e2-db59-4bdf-8ff1-b4f1b6e77c15.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153346/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153346/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/5/9/dataset_559dfd03-c5cc-4df7-a81a-0d1d3242f2d2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153347/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153347/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/9/c/dataset_79c3175d-32aa-42bf-8a95-d342258ca35c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153348/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153348/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/c/5/dataset_6c55e556-9f83-44a0-8c53-9dbf9921639e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153349/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153349/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/5/9/dataset_8590fd6a-6e83-42f1-a8ea-6091048a4fa1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153350/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153350/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/6/8/dataset_26898fcb-3d7d-4e7b-9e41-3a6a04183d03.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153351/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153351/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/8/0/dataset_c8016b7a-f043-451a-b31d-fda9ca52bf42.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153352/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153352/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/d/7/dataset_9d71a9dc-315e-4b7f-8ace-4615b80c2409.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153353/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153353/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/b/1/dataset_2b12a6bf-526d-4b50-89cd-7f5a5f7ef312.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153354/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153354/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/e/0/dataset_0e0c6321-5e38-453d-9915-ab93e165a387.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153355/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153355/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/f/d/dataset_7fd62109-ca78-47a2-96f5-7ab157736420.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153356/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153356/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153356/inputs/dataset_bac20c6d-7416-4c0c-82a5-ff6f1d821b10.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153357/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153357/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/8/4/dataset_984e5ba5-65f3-42e5-9fee-0e12f0ca8aa9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153358/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153358/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/3/5/dataset_235cd3f9-b31a-4be2-b1e5-384cff6ec743.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153359/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153359/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153359/inputs/dataset_628b5d55-4890-41f9-9ffa-7b9b15587571.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153360/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153360/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153360/inputs/dataset_41f535b5-78f0-4db1-a88d-66c5e2a85a9d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153361/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153361/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/e/9/dataset_1e9296a1-62b7-4ba4-b0fa-1457f75eaaaa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153362/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153362/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/3/a/dataset_33a685a9-703e-49a9-ba28-be6691c5223a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153363/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153363/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/5/8/dataset_f5898b7c-8df3-4fbe-b29b-ff6cc5564997.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153364/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153364/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/1/a/dataset_d1a655fd-593e-472d-890b-0af4d1fea370.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153365/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153365/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153365/inputs/dataset_aa5e0dfd-2ac3-4052-bd80-a77851a194c4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153366/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153366/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/9/6/dataset_1967360b-9008-456a-883a-4e2c254e0709.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153367/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153367/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/d/d/dataset_9ddd9a54-7321-4292-bec1-fc83836433aa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153368/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153368/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/9/b/dataset_59b9a0f5-7d49-458f-b09b-d89e6aaba81e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153369/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153369/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/5/4/dataset_754a8672-7042-40d8-8bc4-7b8015722ac6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153370/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153370/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153370/inputs/dataset_52bce548-8975-4a4b-8f3b-2dabec39b483.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153371/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153371/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/2/2/dataset_3227fada-291a-4587-b0e3-bd0a40a40553.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153372/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153372/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/a/3/dataset_ea396d71-32c5-48a0-a2aa-0aee3c1da2f8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153373/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153373/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/3/c/dataset_63c8aff5-9d80-40d3-b61c-f4298f6eac58.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153374/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153374/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153374/inputs/dataset_9d82df52-6221-4eb3-ae03-0a40b977a26f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153375/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153375/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153375/inputs/dataset_8cdb3ebd-06e0-4bf3-9210-8cb113a10a54.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153376/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153376/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153376/inputs/dataset_70dfe9d8-8bcf-48d9-b2cf-da6892a91f67.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153377/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153377/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/e/4/dataset_ae4a14ab-16fb-4aa3-9101-b426ef2424fd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153378/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153378/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153378/inputs/dataset_8e7a4a23-71bd-48b3-beb4-0070e8014fd6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153379/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153379/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153379/inputs/dataset_6bf437a9-cdc6-4d45-8e82-a0d9c2b11a60.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153380/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153380/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153380/inputs/dataset_c0b2b711-4f0f-4ba3-90a3-d9ca77c09aa5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153381/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153381/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153381/inputs/dataset_3be788fd-6fc2-472c-b7d1-e3739b7c7a74.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153382/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153382/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/6/2/dataset_3621944d-8624-467f-a6c5-ad3d730dbcdc.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153383/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153383/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153383/inputs/dataset_7e1d2997-a16b-466b-b486-ea0d2c9f6246.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153384/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153384/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153384/inputs/dataset_069a6aab-9147-418b-be89-5919d1474075.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153385/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153385/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/7/a/dataset_17abdf09-8c46-4a85-b584-39bbcf99b925.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153386/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153386/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/f/0/dataset_cf0770d6-5b4e-46ad-b4c3-bbf695203f16.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153387/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153387/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/6/d/dataset_56d6f3ad-42d1-46ce-ab94-8cdbea1b82c8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153388/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153388/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/3/6/dataset_0368c418-a04e-4662-8252-ce4f9acc38c4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153389/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153389/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/b/7/dataset_ab78d30e-3097-492f-9dc7-1464c24c521b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153390/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72153390/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72153390/inputs/dataset_6e443207-12cb-4b7e-a3e4-6793cac4a57e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153391/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153391/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/e/d/dataset_4ed48225-01da-4b11-b79b-7a0b391bc3dd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153392/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153392/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/5/e/dataset_c5e32b83-11c2-4970-8eba-ab4630b8514e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153393/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153393/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/1/3/dataset_213c27ee-06aa-4795-b783-306a7a1dd19e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153394/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/153/72153394/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/7/dataset_b172e50b-6552-49ca-9fe2-9a761dad0c42.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159566/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159566/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/4/c/dataset_c4c4f542-8eac-4931-a5d3-286e8dea7a87.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159568/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159568/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159568/inputs/dataset_0230eedf-5787-466d-b5b9-1286167fa44a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159571/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159571/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/1/8/dataset_f189de11-a470-4228-a1b4-1265f8cfc411.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159573/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159573/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159573/inputs/dataset_1fdc739c-45b6-4138-b8a5-a07aeb362a4d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159575/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159575/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159575/inputs/dataset_51061859-a2f9-4b2b-9fba-631da2baa80c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159577/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159577/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159577/inputs/dataset_b1cab5c6-f03c-4db1-a710-f38c7354863f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159579/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159579/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/7/9/dataset_e797089c-8244-40cb-b65a-9743337bf462.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159581/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159581/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159581/inputs/dataset_660d6291-f355-45ea-9261-fa333bb1079e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159583/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159583/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159583/inputs/dataset_33a369fa-19c3-46b3-ab6e-a1306deb998f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159585/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159585/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/0/a/dataset_30a13cdf-6dc3-467e-8602-bea55a00a67d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159587/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159587/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159587/inputs/dataset_841e692c-83e5-4cf0-b7d7-d30ac1fd6246.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159589/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159589/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/e/7/dataset_fe7086c3-21e2-4456-839b-50068ac7b2e0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159591/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159591/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/4/3/dataset_343a5971-171f-4317-8619-96bd37485c73.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159593/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159593/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/0/b/dataset_f0b95a85-213a-4135-83a3-41593152d17a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159595/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159595/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/0/e/dataset_e0eeff7d-db00-4eea-9b6b-e680c782c271.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159597/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159597/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/1/3/dataset_013e01ab-dbda-4444-8874-a7268c31070b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159599/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159599/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159599/inputs/dataset_f868478f-3382-4ace-9436-35a03845ae24.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159601/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159601/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/6/b/dataset_66ba8869-58f5-4a06-97ec-70890e503189.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159603/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159603/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/4/1/dataset_241961e6-94e3-43f2-acdb-521870b31b72.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159605/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159605/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/5/4/dataset_954188fa-1c13-4be6-a676-cfbf05b50425.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159607/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159607/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159607/inputs/dataset_2950ec21-676a-41de-b63d-a78b42f688dd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159609/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159609/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/6/1/dataset_161d2eb2-10b9-4a8e-a9e5-c8b969723337.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159611/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159611/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/7/5/dataset_875e9d3b-7437-433b-a8c8-e290898280bd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159614/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159614/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/2/c/dataset_32cc9271-4afb-43cb-b392-51e3e40aa219.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159616/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159616/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/9/f/dataset_39fa78de-acf9-4741-bbc5-92bb83b50094.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159618/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159618/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/3/f/dataset_a3f7068c-66b7-42eb-8006-243f37155abb.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159620/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159620/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/2/0/dataset_020efee2-817d-463d-a09d-bd9b1d22324a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159622/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159622/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/f/6/dataset_cf62e4bd-eb04-477a-b645-e73e6abd84ab.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159624/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159624/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159624/inputs/dataset_bd8b30c7-062d-4313-a4b0-b0227be36dca.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159626/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159626/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/0/2/dataset_7026620b-86ed-48d8-9c61-39f83230bde0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159628/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159628/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/4/0/dataset_440a8562-080c-4e45-bb23-67553438c52d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159630/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159630/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/8/5/dataset_c8595199-9911-488e-a016-112d68479632.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159632/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159632/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159632/inputs/dataset_3d0ac099-3693-400c-8a02-5def9e6b38be.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159634/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159634/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/9/5/dataset_b955d4f3-71f5-4b36-946a-1e5f2ed6ef0b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159636/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159636/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/6/f/dataset_f6f38166-80f0-475a-ade5-155ecf998ca6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159638/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159638/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/b/2/dataset_7b254eca-6653-4f61-8f6f-2c42d8f74292.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159640/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159640/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159640/inputs/dataset_3036630c-8add-4d54-b5bc-3281085e9e81.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159642/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159642/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159642/inputs/dataset_a78709b6-1072-4566-9bdc-fc188b95919f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159644/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159644/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/e/a/dataset_6eaa821b-ff05-4ec8-8db5-f2d772bc5a26.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159646/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159646/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159646/inputs/dataset_265c39cb-25ad-4c83-a1e4-0041aee88e48.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159648/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159648/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/a/c/dataset_3aca6b46-60b1-43b3-97a9-cab1c4e70c7a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159650/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159650/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/f/6/dataset_bf69ecaa-dc9e-4dc3-91fc-dd3b6acee9ea.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159652/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159652/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/1/2/dataset_91252c64-3c09-4716-beb6-8dd46fd52170.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159654/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159654/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159654/inputs/dataset_010287e3-93af-42b5-9908-0b33969c6ef5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159656/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159656/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/8/a/dataset_18a7443a-8813-429e-9009-33191b0f28df.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159658/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159658/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/0/7/dataset_40715477-e846-461e-ab4b-7ca54fa8e70e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159660/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159660/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/5/9/dataset_3597ee84-f534-4afe-bebf-955673229df8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159662/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159662/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/3/4/dataset_b341a51f-ef1e-493b-ba42-89758a2b5405.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159664/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159664/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/c/a/dataset_ecae2656-5f89-4c2f-92e0-7b79162c03eb.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159666/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159666/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/1/8/dataset_61889dc0-fcde-4993-94b5-cc76572035c2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159668/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159668/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159668/inputs/dataset_27d6bb7f-8a56-4a53-88c6-dff75fdaf930.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159670/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159670/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/8/4/dataset_c846adfe-296f-4606-b299-0491c4408c2d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159672/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159672/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/f/4/dataset_9f4847f8-1bc2-4f1f-839b-fa37b1e101f6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159674/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159674/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/7/2/dataset_3720b06d-a5ac-4726-91fe-9dfd9704ae5b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159676/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159676/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/f/e/dataset_ffeef47f-dbe0-44f3-a570-569b0d587836.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159678/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159678/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/d/8/dataset_3d89645f-e9e2-4a19-838a-774362a8924c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159680/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159680/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/a/0/dataset_9a0ef7a8-1258-4141-ab65-e75a7cc2c690.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159682/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159682/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/0/a/dataset_90adddc2-7637-4b80-912f-39e9e3fc5f0f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159684/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159684/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/e/4/dataset_4e4dfc18-97dd-4d3f-bacf-e55a97a9dab6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159686/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159686/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/c/9/dataset_3c9cfc67-895c-4fde-9bed-8e230d756295.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159688/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159688/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159688/inputs/dataset_72e289dd-f924-4061-b416-9c83f07c7520.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159690/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159690/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/4/9/dataset_549fabb5-b4b1-4367-9235-b9d5ede20e4f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159692/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159692/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159692/inputs/dataset_36441ef5-a7fd-46f2-a423-396ef9a3f1cd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159694/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159694/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/b/5/dataset_ab54aff1-f2f9-404a-b239-f75b58b57891.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159696/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159696/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/e/d/dataset_8ed6530c-d63e-4825-bea6-19e136db0f9a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159698/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159698/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/2/4/dataset_024148f4-e2da-4017-bd52-bebd8842a22e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159701/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159701/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/1/c/dataset_61c9fc09-7208-40bf-9610-4cd746972690.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159703/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159703/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/9/7/dataset_597cc2e3-63db-42c6-a433-c9c2e26e6a6a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159705/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159705/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/2/3/dataset_c23b421d-877c-4ab1-9b4b-96f8f41373e7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159707/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159707/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/2/1/dataset_c21b33cc-4ea0-4a69-a812-2bc48accfb97.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159709/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159709/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/7/b/dataset_07baa265-10e5-4637-9a62-adeb0a92127e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159711/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159711/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/0/4/dataset_e04bcb38-bb86-4c05-8448-66d085b1c859.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159713/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159713/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/2/a/dataset_72ac6289-b8f8-41ce-983f-c7b9f21531ca.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159715/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159715/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/e/a/dataset_ceaef0d2-81da-42ad-bea8-19f85ea407b0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159717/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159717/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159717/inputs/dataset_9dce7390-d5b2-47d9-a72b-eb25c71924ef.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159719/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159719/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/0/6/dataset_3061a706-9c6f-45cb-be7b-ff0fba5497e0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159721/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159721/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/2/8/dataset_428b103f-ed96-4130-b9a6-0d64e1fa9e32.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159724/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159724/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159724/inputs/dataset_6dbb9eb0-736f-49d7-9103-ae3f484a8c66.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159726/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159726/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/4/c/dataset_34c18c66-a612-4e6a-a728-dca9a2fd7588.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159728/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159728/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/d/d/dataset_5dd7e620-d161-43c5-bc2a-57d37aba5872.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159730/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159730/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/9/dataset_439b5ad1-be27-40f5-a175-5078fe49b978.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159732/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159732/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/7/8/dataset_c785b284-9b77-470f-be94-bcff59765c55.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159734/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159734/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/2/b/dataset_52b1cf85-7dab-4c37-bc6f-4ea45aa9d85e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159736/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159736/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/e/8/dataset_5e810531-9368-4cb1-9114-1360f0c96e91.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159738/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159738/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159738/inputs/dataset_8d8460b2-97d1-4b72-9b78-5d61afdad454.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159740/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159740/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/e/8/dataset_1e8e0d7e-1d40-479b-8b1e-61241d983582.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159742/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159742/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159742/inputs/dataset_00d2612d-02c4-42ac-9ecb-258387a6c3a5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159744/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159744/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/7/1/dataset_77198980-f8c7-4cf3-9cca-34e40a0c12cb.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159746/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159746/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/3/9/dataset_239b4b43-47e5-4fde-ad3f-6545d3d8bc66.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159748/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159748/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159748/inputs/dataset_18bbcab8-d512-40b6-a1bb-41ae51d4430c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159750/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159750/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/8/3/dataset_883d97a1-1da5-434a-8586-b09496aaaea7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159752/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159752/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/1/dataset_b118fa30-b6c2-44c9-b9ef-5af15b6e9690.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159754/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159754/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/7/a/dataset_c7aeae65-61b7-42a6-8b05-e065b9b92e62.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159756/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159756/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/5/3/dataset_353d67c5-5304-4313-b84f-185e1b7c4ef2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159758/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159758/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/7/f/dataset_57ff921f-838a-4942-8fe5-d1be252c52e9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159760/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159760/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159760/inputs/dataset_63cc9628-4c35-4c2d-a560-ec21651c9394.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159762/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159762/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/c/f/dataset_2cf8b4df-d16a-479f-a69e-e2bd82b7896b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159764/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159764/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159764/inputs/dataset_36e1bdca-5167-47d3-88e5-2676e99d8234.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159766/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159766/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/7/1/dataset_67147017-77d7-400d-b9df-38a0157c186c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159768/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159768/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/c/2/dataset_ec216ea7-4e66-4194-9a87-962735094655.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159770/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159770/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/4/5/dataset_0454c5cf-0f88-4ad3-8409-699abe9245e7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159772/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159772/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159772/inputs/dataset_6d9e5a56-2fc5-4639-9c0f-9eb5b6a56329.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159774/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159774/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/8/6/dataset_b86490a3-9468-47a7-928c-f27f13c0ea0c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159776/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159776/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159776/inputs/dataset_70f3f40e-cd04-4715-a9bb-f39efb355a56.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159778/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159778/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159778/inputs/dataset_e31064d7-1ecd-4a88-a1b0-4f4d7bfd09b2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159780/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159780/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159780/inputs/dataset_838f2810-ae45-4908-b65c-65657a5cbff9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159782/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159782/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/4/f/dataset_74f6d8ff-2d0b-49d5-859c-eb2bc4185a54.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159784/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159784/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/b/8/dataset_0b8a30a5-111e-4a48-b352-f423830230b9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159786/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159786/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/f/dataset_43f01c0a-4664-4eaf-b05f-5ce9e974b7c4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159788/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159788/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/8/5/dataset_585476b1-0e1b-4617-81d7-5b2a8328a48a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159791/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159791/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/b/7/dataset_8b7bb581-3407-4563-a7be-011aeb2f6a62.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159793/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159793/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/e/b/dataset_cebdd2db-7357-4ff1-8446-f166b39cc881.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159795/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159795/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/5/2/dataset_552fc282-4435-4d24-bf0b-4ed5484b9135.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159798/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159798/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/7/3/dataset_c7327645-c403-469e-bafd-63b9013ac451.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159801/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159801/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/6/0/dataset_a60a20e6-b2f0-4a93-a6e2-41acc04d5ca6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159803/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159803/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/9/b/dataset_c9b3d948-37b2-4314-9565-27de1ae6b874.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159805/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159805/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159805/inputs/dataset_fb6b3123-ed8a-46d3-94d9-39f9085e0329.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159807/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159807/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/d/9/dataset_cd973bda-3fe4-41f5-b5fd-48e0906e7145.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159809/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159809/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/d/c/dataset_cdcf7373-c5e3-41fe-8582-64e85ab87b4d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159811/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159811/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/4/6/dataset_b46bffe8-9845-4caf-86be-27555a4e3108.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159813/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159813/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159813/inputs/dataset_d6bc9f03-0cdf-4387-890a-4a3ba7538b6e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159815/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159815/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/1/1/dataset_1115e405-ae3b-450c-9050-e19d4ceb16ce.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159817/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159817/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/5/4/dataset_6543be0d-28c3-42ad-864f-c478fddf46da.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159819/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159819/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159819/inputs/dataset_e8eed609-fd7e-4894-9d14-6044d4530d6a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159821/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159821/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159821/inputs/dataset_9d741165-b474-4e6f-a443-7b3b14b3274b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159823/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159823/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/2/4/dataset_92400ff8-5334-4ce6-afda-9802470357b1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159825/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159825/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159825/inputs/dataset_34a325c2-7de7-4ef5-b69b-2058d370ed0c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159827/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159827/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/4/6/dataset_d46788b8-274f-4c31-8eee-d2b5684e9194.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159829/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159829/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/f/5/dataset_cf57af57-97b7-4081-94c5-090d603152b2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159831/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159831/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159831/inputs/dataset_ae68926a-db7e-4c13-9e32-481ccbcdf56d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159833/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159833/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/9/9/dataset_a999cc7d-840e-4b67-8eff-c4d1aef46abf.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159835/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159835/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/6/9/dataset_06932bee-9c57-47cd-981c-1911fdb59444.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159837/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159837/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159837/inputs/dataset_9bb07e93-ec36-4086-97ba-aa5dc624cd84.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159839/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159839/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/8/6/dataset_c86b9e37-5a86-4d67-a0cc-6d38142291ca.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159841/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159841/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/8/e/dataset_68e952ff-7ec6-466c-9aa0-0b00b2df686a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159843/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159843/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/2/1/dataset_221aa7b4-0ae1-41e8-b584-fa30c62e5910.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159845/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159845/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/3/c/dataset_93c6de1b-3e2d-4194-838e-7095071d2273.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159847/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159847/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/7/7/dataset_0777a56f-6124-4d92-9b4d-eecdd79ee71e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159849/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159849/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/1/6/dataset_116f9f5e-b24a-494c-a958-0f769c1ecd0d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159851/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159851/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/2/8/dataset_e28d6010-e430-4b95-b7a6-4d323e7fa50e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159853/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159853/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/8/f/dataset_e8ff7f68-c14e-48c2-9d37-9b36d012e49a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159855/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159855/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/f/3/dataset_df3f2826-403c-46db-b50f-f3f14aa7ecd0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159857/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159857/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/f/a/dataset_cfa2e6f0-7c9d-467e-9e97-527b5990bbd8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159859/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159859/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159859/inputs/dataset_2be63fb9-e011-48c5-9177-7a2f5eb2855f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159861/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159861/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/b/8/dataset_6b839bd6-a9ef-4fc6-a2aa-7a7e851bd385.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159863/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159863/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159863/inputs/dataset_87db670f-d1bb-438c-8126-cbcd0baf3795.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159865/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159865/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/4/8/dataset_5481a5e8-a93f-43bd-a149-93c4454294fa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159867/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159867/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/4/5/dataset_f4561595-44f4-412e-8f1c-5d48cf5454e8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159869/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159869/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/1/6/dataset_d164a579-7a2a-4ee0-908b-9ac15a7cb219.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159871/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159871/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/7/f/dataset_87fd87bc-1ece-4621-902e-72695be124b4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159873/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159873/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159873/inputs/dataset_c75c4fd3-0a1d-47f9-bac6-14d7fba55233.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159875/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159875/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159875/inputs/dataset_066ed8a2-092c-468b-8e63-ad3b2097e334.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159877/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159877/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/3/d/dataset_d3d4a0a0-57e4-4c7a-b637-683a42d28603.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159879/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159879/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159879/inputs/dataset_b971d5d2-e6b1-4364-9734-c9caad8dc955.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159881/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159881/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/8/c/dataset_08cfe6d7-d8b6-4f4b-a5b8-1a42591fc3cf.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159883/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159883/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/0/8/dataset_908d09e5-0d71-4f97-b4d0-da433b99ebfc.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159885/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159885/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/7/2/dataset_0728aabb-13bc-40ee-afaa-c41ce285f2f4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159887/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159887/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/e/6/dataset_ee683dca-df3c-4e9a-8e88-9bbce9a82038.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159889/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159889/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/8/c/dataset_38ce21fb-a423-40c4-a45d-d5592a11f001.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159891/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159891/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/f/6/dataset_bf61be0b-c99a-4bde-8c27-aed3a8977160.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159893/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159893/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/3/2/dataset_332fa420-5eab-4f71-a3a8-83fce8f51c21.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159895/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159895/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/3/1/dataset_931bb7b2-7e28-47ed-b16e-d5caefbd3bbf.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159898/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159898/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/e/2/dataset_7e2807ae-9c5a-440a-95a5-9cc60a9aa479.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159900/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159900/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/c/f/dataset_bcfdacfb-b973-4c62-a74f-b74d3fe790ba.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159902/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159902/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/a/7/dataset_fa76b2e8-bca5-44e3-9d97-83cae59e6639.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159904/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159904/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/d/1/dataset_fd11b9d7-6bd5-4f06-9d59-ef1e4ffb2d81.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159906/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159906/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159906/inputs/dataset_1d444132-d98b-4709-9bb5-47076c87e1b8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159908/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159908/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/c/4/dataset_1c431b45-aee2-4078-9181-2dffbae06c4d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159911/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159911/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/e/0/dataset_ee0b4645-adbd-422b-bb5b-9ec86cf83fed.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159913/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159913/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/9/b/dataset_69b3e00f-0848-426e-8bf9-9784b7d66837.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159915/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159915/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/e/c/dataset_2ec40f57-db71-49f0-81a6-3a2d9b052c5a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159917/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159917/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/4/8/dataset_848e9de7-111a-4e06-ba54-b02aabc7a701.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159919/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159919/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/b/5/dataset_8b582e88-23d9-4781-8c97-0954b4bbd5a1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159921/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159921/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/8/dataset_b1885c44-6869-499d-aff0-de4373e8f461.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159923/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159923/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/3/6/dataset_8361224b-9dc3-4a0e-bf66-e020ff5ba027.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159925/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159925/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/7/f/dataset_c7f95038-3f9c-4bcb-b1b6-e1b1030f4e5a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159927/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159927/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159927/inputs/dataset_2a52a75a-2361-453e-a5a5-6b8c0a9ca041.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159929/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159929/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/f/d/dataset_bfd34714-6b7e-4e22-bcdc-392675e09b98.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159931/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72159931/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72159931/inputs/dataset_4e427da1-cab7-4790-b2f0-84348e6a7b62.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159933/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159933/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/d/f/dataset_8df7310d-0dce-4d6c-9228-64cc135808a9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159935/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159935/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/6/b/dataset_86bc1ff2-c389-46c6-a7ad-a92736b8bade.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159937/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159937/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/7/5/dataset_a7527ce4-464b-4179-bbf4-9826ce2ea7bd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159939/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159939/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/1/b/dataset_61b58da0-85be-464b-9dd9-fb1f55c40be6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159941/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159941/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/3/f/dataset_53fd67f2-61e0-4e80-8c11-097ee0e9c539.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159943/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159943/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/9/8/dataset_9985fb21-12ca-45e7-a2f5-8dbc742e54ab.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159945/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159945/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/a/4/dataset_4a4451f5-02d4-4dc0-ab2b-40c79c7991f1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159947/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159947/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/8/7/dataset_f87d3dc6-eb10-4d69-ae09-aff6dbda091c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159949/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159949/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/3/5/dataset_93595167-2e65-4d37-aeb8-5e6be3e8ed3b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159951/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159951/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/c/8/dataset_dc8fcc5a-6b44-4705-b70c-9fdd070a466b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159953/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159953/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/a/1/dataset_6a1c551b-8f90-439c-816a-e3d1f6b9dcfa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159955/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159955/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/4/2/dataset_142f206d-dd18-4ef6-9ba0-c2f96395dff2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159957/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159957/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/e/e/dataset_aee0299c-e275-4ed0-bca0-54a1626aca61.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159959/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159959/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/2/b/dataset_62b73436-4d79-4c51-bb81-330a1428f250.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159961/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159961/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/1/3/dataset_1131568d-fa7d-4c14-930e-a4c5d63af716.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159963/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159963/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/8/8/dataset_d888c322-8040-4762-a4df-be0ce73b2e50.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159965/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159965/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/2/6/dataset_12608759-6651-428f-b809-154fba926522.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159967/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159967/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/2/e/dataset_f2eadf94-c6a3-4e1a-aa2b-b61956b4cbea.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159970/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159970/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/2/5/dataset_b25737c5-da59-4f22-aea2-03dcb291ce0c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159972/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159972/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/7/1/dataset_171dfef3-042f-4ed7-a1f3-740bcf2a241d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159974/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/159/72159974/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/1/5/dataset_d157ee38-7de6-482d-a576-5fbff654e618.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161152/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161152/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72161152/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72161152/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72161152/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72161152/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72161152/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161235/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161235/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72161235/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72161235/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72161235/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72161235/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72161235/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161277/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161277/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i vcf -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/7/dataset_b172e50b-6552-49ca-9fe2-9a761dad0c42.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161426/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161426/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/9/5/dataset_d95bc63b-664e-434d-b624-651aa6086d69.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161427/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161427/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/f/0/dataset_df094e4d-2e23-4efa-8827-2c4502631cd6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161428/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161428/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/0/1/dataset_a010f1a7-cd22-441e-8caa-5475bc975b1f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161429/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161429/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/d/6/dataset_cd6f0597-9714-4034-9363-e77c2700942c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161430/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161430/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/9/c/dataset_79c5b693-efd9-45de-9e4d-0bf6a4f8e5d0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161431/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161431/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/3/2/dataset_032cdd87-6977-4f0e-be0f-487d3a697f28.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161432/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161432/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/5/b/dataset_25bc3faf-bc0a-4303-9cee-0ca4740c8581.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161433/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161433/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/9/5/dataset_a95c6115-1078-46d9-b47b-2d1bad986705.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161434/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161434/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/b/9/dataset_2b9afd15-9459-462e-b1c9-b87e48ed12b4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161435/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161435/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/a/dataset_b1a15c3a-d9f2-4dab-bc97-2be24e862454.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161436/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161436/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/d/3/dataset_5d30e132-4994-47a1-9418-8584c777d000.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161437/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161437/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/3/4/dataset_c342e438-8117-4038-b719-585a78e2fc9d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161438/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161438/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161438/inputs/dataset_b68dd060-568a-489c-93ad-40769f1a2c51.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161439/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161439/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/0/7/dataset_6079ccbe-52ae-40db-b425-8e426d5a9b07.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161440/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161440/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/d/9/dataset_bd91e2a4-2fd9-4ce2-802c-138d93f00e1b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161441/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161441/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/b/7/dataset_bb7e479c-2f29-43bc-a3a4-5d9ffb9df839.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161442/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161442/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/0/2/dataset_e025028e-9ca7-4bf7-a946-f44cc9601861.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161443/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161443/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/2/5/dataset_525679d2-8c3f-44cd-baf5-f82c09cbedf8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161444/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161444/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/8/2/dataset_682ec1fa-3ff8-47c8-a931-fb3a4bc1f13a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161445/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161445/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/2/9/dataset_0298aa6a-979f-4704-8e4d-aff9df4c7f24.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161446/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161446/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/5/5/dataset_a55f0881-395e-4488-a9d9-712b6df50a9f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161447/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161447/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/f/f/dataset_bff3dd72-ec63-455f-904a-24b102f33a10.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161448/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161448/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/3/1/dataset_7314aabd-c838-4249-950d-a57368968dcf.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161449/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161449/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/f/d/dataset_6fd8baf7-6906-4b4d-bdbd-fdae75c0881b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161450/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161450/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/8/0/dataset_980f32e1-c81f-4df9-b7c6-d397273e2d09.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161451/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161451/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/0/0/dataset_000f0226-745a-472f-940c-452a5886f0f0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161452/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161452/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/8/d/dataset_28d32649-6437-4870-a3c2-e253bafbce47.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161453/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161453/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/f/4/dataset_df43efdd-f67a-4648-bc2a-c3c37c4f554e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161454/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161454/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/5/dataset_435680d3-035b-417c-b93e-f172799647fb.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161455/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161455/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/0/0/dataset_100c9fc4-fb66-4fad-bb38-f4be4bf0f1d8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161456/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161456/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/3/e/dataset_83e7e872-1536-47ae-a183-382d67855335.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161457/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161457/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/2/7/dataset_3274ba1f-1c55-4818-a543-8d4314d02aee.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161458/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161458/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/4/8/dataset_748e529f-2e0e-4675-be53-4809bc78ede6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161459/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161459/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/d/d/dataset_6dd95ea3-95ba-4368-b88f-da48f4636975.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161460/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161460/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/8/4/dataset_68470bd7-1577-460e-84f6-4c98475fd3a0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161461/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161461/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/0/3/dataset_203c279f-c434-4f98-afb5-e43aebc24fb5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161462/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161462/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/1/8/dataset_618a811d-e41f-4f17-923a-a9a56cdbd115.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161463/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161463/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/3/f/dataset_13fcc053-4e4d-4ac6-a756-1c4d9dc8e636.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161464/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161464/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/f/6/dataset_6f6d3c67-84cf-4890-9285-e13ea3f77ad3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161465/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161465/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/9/c/dataset_39cdbddf-1973-4244-b4dd-2e1ee9445ca8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161466/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161466/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/f/5/dataset_0f5044da-5395-4448-b7eb-ee638fb3ce04.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161467/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161467/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/d/3/dataset_ed3c9656-10c7-4fce-9bf7-8545e64d0667.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161468/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161468/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/5/6/dataset_f56b6194-0ade-4eab-874b-e66051251e2e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161469/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161469/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/f/7/dataset_df7516fe-4bd9-41dd-a1f3-2060fe9250d0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161470/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161470/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/f/3/dataset_6f3bfc62-cee5-4179-ba35-255e7799acea.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161471/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161471/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/0/5/dataset_805b8071-d1e5-4ac1-b7c4-763331ecaea6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161472/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161472/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/b/9/dataset_9b9c6457-20b2-4f1b-b734-8ce1759fe6b5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161473/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161473/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/4/d/dataset_34d06fa1-c2b8-4ded-a4cb-1fe92dd86d83.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161474/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161474/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/9/4/dataset_a94dccac-0300-465b-ae65-0a654178dea0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161475/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161475/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/8/3/dataset_d831f973-52e4-48fc-a601-8cb37e5abed3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161476/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161476/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/b/7/dataset_6b70a991-3675-45c0-be5c-e80ef05a0a01.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161477/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161477/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/6/d/dataset_16d548dc-8592-4b4b-85ab-ef360f288692.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161478/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161478/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/6/a/dataset_36af28e6-0518-4957-9c08-3f394f994c20.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161479/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161479/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/9/e/dataset_69e4442c-ef18-44d1-9157-ece70535283d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161480/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161480/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/8/0/dataset_080bc15e-8925-473e-9724-aec9006189bc.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161481/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161481/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/c/c/dataset_fcc33685-3cec-41b9-870d-241cc281ebaa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161482/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161482/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/e/a/dataset_bea42387-35c3-4a63-9f2f-5e81aa7e9bd1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161483/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161483/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/0/5/dataset_305bab1b-1a38-48a9-9a9f-512da3c289af.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161484/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161484/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/0/e/dataset_c0e723d2-0882-4da8-b278-8fcacd073539.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161485/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161485/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/6/1/dataset_9617a65c-400b-4f5c-ac52-19e22eb30721.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161486/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161486/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/9/6/dataset_196b5699-ed25-44bd-84eb-b063ceb4259e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161487/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161487/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/d/7/dataset_ad780b1d-af86-4f9a-93fa-e878be00885a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161488/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161488/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/d/7/dataset_cd7c6b46-70b4-467a-8851-06b479cb9814.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161489/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161489/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/3/f/dataset_f3f15bd9-c8be-4102-afa3-5e48b5c29366.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161490/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161490/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/0/3/dataset_703cb53e-6e81-43dd-8fed-787e549af33c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161491/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161491/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/a/a/dataset_2aab484e-b4b9-49c6-97f3-ce2bb7ae5eda.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161492/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161492/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/b/1/dataset_6b186dc6-95eb-436a-9fff-7a2dcda25ab4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161493/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161493/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/f/1/dataset_0f16da8a-2a10-4ce4-b673-625c9e77f72b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161494/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161494/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161494/inputs/dataset_e9458c2d-51bd-4ae3-beda-f17ff35d82b1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161495/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161495/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/a/3/dataset_fa36a54c-b45f-4c76-9401-539917e58851.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161496/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161496/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/7/dataset_b17eb3c2-7f36-42be-b19b-732f2d5e5727.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161497/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161497/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/3/6/dataset_136da2e3-836c-4630-ad71-96f95e304d1c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161498/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161498/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/2/9/dataset_929fa0e8-eee4-45ff-99e6-eaf707e18bab.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161499/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161499/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/2/f/dataset_72fa2777-4641-4ab9-b516-b696df1c4236.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161500/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161500/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/a/f/dataset_0aff25a5-2964-4cdd-84e6-d0b0c400a6a8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161501/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161501/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/e/7/dataset_ce7ac756-4dc7-44e0-be41-ef711be9501a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161502/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161502/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/2/1/dataset_b21c9ebe-2a08-4cca-a3c6-b8e93a17a398.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161503/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161503/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/e/d/dataset_fed0bace-c05a-4615-a5a2-42b3d0a12f35.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161504/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161504/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/4/d/dataset_e4d24101-f420-4c61-b1e8-6d53cf60e538.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161505/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161505/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/3/d/dataset_a3d0b904-4340-4a56-a3ba-0a7a3b083b0b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161506/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161506/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/8/d/dataset_b8d00513-d19f-4e58-8d8b-a75f56c96835.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161507/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161507/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/8/2/dataset_b82a960d-5048-486e-b590-22670ab66fb0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161508/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161508/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/7/d/dataset_47d6504a-b329-44fc-8bfb-562155a66280.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161509/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161509/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/e/3/dataset_de3ff80c-68e8-450e-b8e5-bd7e47341fa8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161510/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161510/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161510/inputs/dataset_e05df72a-a702-4ff1-993e-1cddcb73d83f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161511/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161511/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161511/inputs/dataset_c44e7f63-3e0a-4ede-a0f1-7592edbec187.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161512/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161512/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/3/8/dataset_d3837626-f485-4cab-9f84-6254fce47169.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161513/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161513/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/1/1/dataset_911b24a0-6c86-42b4-b682-72d9566f45ea.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161514/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161514/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/2/d/dataset_72d58135-e64e-453e-9cd0-14bb18d46405.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161515/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161515/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/a/5/dataset_fa5bb06b-ec8c-4978-b920-0f3cd515d25e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161516/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161516/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/4/5/dataset_b45f97fd-e9b0-486e-a4d7-5031847de6c6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161517/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161517/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/7/0/dataset_170b312a-7e91-4af3-9d74-40fe0b5626d7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161518/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161518/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/f/1/dataset_7f1699a0-665d-4381-a019-fda6a2b57660.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161519/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161519/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161519/inputs/dataset_20ecb23f-22bf-49ee-8781-b05f6afe3254.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161520/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161520/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161520/inputs/dataset_484775d8-04c9-4a2b-bd15-a164d96ff166.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161521/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161521/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161521/inputs/dataset_3cadf0c0-d87d-4793-843e-abe92364b4b2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161522/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161522/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/5/4/dataset_b54990a3-b01f-48bb-a411-914d1beb503d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161523/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161523/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/5/b/dataset_55b1f1bd-95b9-4f76-9af8-21779da3fea3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161524/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161524/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/9/e/dataset_09ee83c0-0eb9-42e3-8361-41a43cc1fd09.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161525/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161525/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/4/d/dataset_74d26f0c-83ea-458f-99a1-f1acfd3126fe.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161526/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161526/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/9/8/dataset_39871360-579f-4b86-b09f-c26c6911dce6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161527/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161527/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/2/0/dataset_0203aa02-98d8-484a-866e-2d63c31f5bf0.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161528/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161528/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/5/0/dataset_e50c355d-80f1-421e-8755-f8b06cb067a3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161529/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161529/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/3/a/dataset_f3a91be2-1251-48b8-ab45-e8de9fd5aeca.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161530/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161530/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/2/b/dataset_92b82171-2f79-471e-b821-e51c0839e4ba.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161531/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161531/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/2/e/dataset_92e8dce9-1ea3-4199-91fd-ea947d483c65.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161532/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161532/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/f/d/dataset_bfd22c3b-21df-4aef-bafe-d873f412b493.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161533/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161533/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161533/inputs/dataset_40669698-2e79-410d-9799-fbf4c87d9000.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161534/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161534/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/0/f/dataset_30f25e71-dc28-4f24-a849-bfc760d691b7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161535/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161535/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161535/inputs/dataset_ce114631-f989-4439-9f35-65c25f299047.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161536/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161536/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/9/d/dataset_79d41f5a-8bd2-42d4-8bfa-259246913175.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161537/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161537/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161537/inputs/dataset_588e3fe1-fb14-49dd-a081-9ed57a98629d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161538/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161538/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/b/7/dataset_8b773848-6ba2-4176-b8be-b64d4ac9ff9c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161539/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161539/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/0/1/dataset_a01e64ca-9b01-4c23-82ac-982bbdbf1fd1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161540/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161540/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161540/inputs/dataset_a86b81ba-4c6a-40c1-b5c2-2c73e0c70162.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161541/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161541/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/5/3/dataset_253bd1f8-e0a4-411d-8604-59236db1d362.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161542/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161542/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/e/5/dataset_8e5fd47d-a2a5-4363-b5de-96345aefbd6e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161543/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161543/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/9/8/dataset_9989e108-702f-41ad-a79e-fa4b800df59f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161544/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161544/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/3/dataset_433b8f1d-3aea-4250-a463-984641f1eca8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161545/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161545/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/2/1/dataset_b210a752-144c-452e-a142-1def770f9b0c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161546/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161546/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/e/1/dataset_6e191760-d84c-4901-b98c-f7616129ccde.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161547/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161547/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/b/2/dataset_4b2fe6fd-3164-4196-b0a7-866de4459649.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161548/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161548/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/0/f/dataset_20f7f57c-eb37-49e8-a44e-f77636fa6ef7.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161549/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161549/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/b/3/dataset_7b3b984e-d3ef-4e43-a9c5-a25341f0f82c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161550/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161550/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/a/e/dataset_9aebdca8-c723-410f-a753-2d371b652718.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161551/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161551/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/6/4/dataset_a64d47b6-f625-4e4b-98d2-adce48d0854d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161552/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161552/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/4/7/dataset_9476225d-5e1d-4d6b-a1bd-3460f92d46ad.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161553/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161553/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/0/9/dataset_609f4722-a888-4edf-a41c-596a4867e775.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161554/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161554/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/c/e/dataset_bce3e5b0-4b67-43e6-b842-fe7532a6b08a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161555/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161555/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/b/8/dataset_eb833405-50d8-4dd5-8994-abb9bb68d2a3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161556/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161556/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/3/f/dataset_43f4f717-a60f-47cb-a469-0f506b767741.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161557/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161557/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/5/7/dataset_55758889-b6b7-4116-9889-0ee904de7852.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161558/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161558/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/9/3/dataset_e93b9985-39ba-4b11-a4c8-822ff396a2c4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161559/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161559/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/2/b/dataset_52b11c96-5359-48d3-bd2d-931265337dc9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161560/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161560/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/1/d/dataset_61d432db-b5f7-48a0-82ed-17eda6f45f56.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161561/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161561/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/0/0/dataset_9009e613-f3e1-4232-a6df-f63fe20e4b86.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161562/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161562/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161562/inputs/dataset_879fc460-1902-425f-9789-657a0132d9ee.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161563/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161563/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161563/inputs/dataset_ab6c9f8a-114b-4b0a-acfa-88e428cf3b18.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161564/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161564/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/6/9/dataset_f695bddb-13d7-4334-a0b7-14b92393a800.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161565/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161565/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161565/inputs/dataset_3b28d707-46dd-42e1-a890-a876f624ea01.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161566/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161566/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/1/6/dataset_516f8704-c155-4e1d-86cf-9cb1fa83590b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161567/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161567/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/8/8/dataset_e88f14fc-f2e9-4510-b494-8e08abce3560.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161568/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161568/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/6/7/dataset_06797006-7a2b-481f-8bd3-17661136374d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161569/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161569/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161569/inputs/dataset_2d3368b5-58f0-4df5-91ae-cf94ff2af66a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161570/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161570/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/6/c/dataset_16cafcf3-11d4-4a05-8889-f101903f434d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161571/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161571/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/7/2/dataset_87228687-a3f9-4e58-a00e-2a9aec8661a3.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161572/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161572/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/7/d/dataset_a7d16002-5e34-48e6-addd-a4549e287893.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161573/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161573/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/0/6/dataset_d06010ea-756d-4529-ae30-7eda57090e1a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161574/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161574/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161574/inputs/dataset_e9afad24-6b42-4f29-a0b2-f1af3226e9aa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161575/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161575/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/a/0/dataset_ba06ebb7-40da-4560-9128-07dc8b281c64.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161576/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161576/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/7/1/dataset_571a87e2-db59-4bdf-8ff1-b4f1b6e77c15.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161577/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161577/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/5/9/dataset_559dfd03-c5cc-4df7-a81a-0d1d3242f2d2.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161578/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161578/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/9/c/dataset_79c3175d-32aa-42bf-8a95-d342258ca35c.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161579/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161579/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/c/5/dataset_6c55e556-9f83-44a0-8c53-9dbf9921639e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161580/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161580/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/5/9/dataset_8590fd6a-6e83-42f1-a8ea-6091048a4fa1.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161581/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161581/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/6/8/dataset_26898fcb-3d7d-4e7b-9e41-3a6a04183d03.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161582/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161582/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/8/0/dataset_c8016b7a-f043-451a-b31d-fda9ca52bf42.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161583/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161583/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/d/7/dataset_9d71a9dc-315e-4b7f-8ace-4615b80c2409.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161584/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161584/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/b/1/dataset_2b12a6bf-526d-4b50-89cd-7f5a5f7ef312.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161585/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161585/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/e/0/dataset_0e0c6321-5e38-453d-9915-ab93e165a387.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161586/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161586/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/f/d/dataset_7fd62109-ca78-47a2-96f5-7ab157736420.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161587/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161587/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/a/c/dataset_bac20c6d-7416-4c0c-82a5-ff6f1d821b10.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161588/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161588/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/8/4/dataset_984e5ba5-65f3-42e5-9fee-0e12f0ca8aa9.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161589/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161589/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161589/inputs/dataset_235cd3f9-b31a-4be2-b1e5-384cff6ec743.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161590/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161590/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161590/inputs/dataset_628b5d55-4890-41f9-9ffa-7b9b15587571.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161591/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161591/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/1/f/dataset_41f535b5-78f0-4db1-a88d-66c5e2a85a9d.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161592/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161592/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/e/9/dataset_1e9296a1-62b7-4ba4-b0fa-1457f75eaaaa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161593/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161593/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/3/a/dataset_33a685a9-703e-49a9-ba28-be6691c5223a.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161594/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161594/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/f/5/8/dataset_f5898b7c-8df3-4fbe-b29b-ff6cc5564997.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161595/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161595/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/d/1/a/dataset_d1a655fd-593e-472d-890b-0af4d1fea370.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161596/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161596/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/a/5/dataset_aa5e0dfd-2ac3-4052-bd80-a77851a194c4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161597/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161597/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161597/inputs/dataset_1967360b-9008-456a-883a-4e2c254e0709.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161598/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161598/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/d/d/dataset_9ddd9a54-7321-4292-bec1-fc83836433aa.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161599/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161599/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/9/b/dataset_59b9a0f5-7d49-458f-b09b-d89e6aaba81e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161600/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161600/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/5/4/dataset_754a8672-7042-40d8-8bc4-7b8015722ac6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161601/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161601/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/2/b/dataset_52bce548-8975-4a4b-8f3b-2dabec39b483.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161602/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161602/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/2/2/dataset_3227fada-291a-4587-b0e3-bd0a40a40553.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161603/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161603/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/e/a/3/dataset_ea396d71-32c5-48a0-a2aa-0aee3c1da2f8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161604/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161604/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161604/inputs/dataset_63c8aff5-9d80-40d3-b61c-f4298f6eac58.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161605/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161605/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/9/d/8/dataset_9d82df52-6221-4eb3-ae03-0a40b977a26f.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161606/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161606/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/c/d/dataset_8cdb3ebd-06e0-4bf3-9210-8cb113a10a54.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161607/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161607/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/0/d/dataset_70dfe9d8-8bcf-48d9-b2cf-da6892a91f67.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161608/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161608/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/e/4/dataset_ae4a14ab-16fb-4aa3-9101-b426ef2424fd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161609/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161609/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/8/e/7/dataset_8e7a4a23-71bd-48b3-beb4-0070e8014fd6.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161610/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161610/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/6/b/f/dataset_6bf437a9-cdc6-4d45-8e82-a0d9c2b11a60.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161611/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161611/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161611/inputs/dataset_c0b2b711-4f0f-4ba3-90a3-d9ca77c09aa5.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161612/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161612/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/b/e/dataset_3be788fd-6fc2-472c-b7d1-e3739b7c7a74.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161613/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161613/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/3/6/2/dataset_3621944d-8624-467f-a6c5-ad3d730dbcdc.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161614/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161614/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/7/e/1/dataset_7e1d2997-a16b-466b-b486-ea0d2c9f6246.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161615/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161615/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/6/9/dataset_069a6aab-9147-418b-be89-5919d1474075.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161616/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161616/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/1/7/a/dataset_17abdf09-8c46-4a85-b584-39bbcf99b925.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161617/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161617/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/f/0/dataset_cf0770d6-5b4e-46ad-b4c3-bbf695203f16.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161618/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161618/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/5/6/d/dataset_56d6f3ad-42d1-46ce-ab94-8cdbea1b82c8.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161619/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161619/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/0/3/6/dataset_0368c418-a04e-4662-8252-ce4f9acc38c4.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161620/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161620/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/a/b/7/dataset_ab78d30e-3097-492f-9dc7-1464c24c521b.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161621/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72161621/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /jetstream2/scratch/main/jobs/72161621/inputs/dataset_6e443207-12cb-4b7e-a3e4-6793cac4a57e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161622/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161622/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/4/e/d/dataset_4ed48225-01da-4b11-b79b-7a0b391bc3dd.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161623/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161623/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/c/5/e/dataset_c5e32b83-11c2-4970-8eba-ab4630b8514e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161624/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161624/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/2/1/3/dataset_213c27ee-06aa-4795-b783-306a7a1dd19e.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161625/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/161/72161625/tmp -Xmx11059m -Xms256m
Error : Canccer annotation is only supported when when output is in VCF format
Command line : SnpEff -i bed -o bed -formatEff -classic -sequenceOntology -noShiftHgvs -noHgvs -geneId -oicr -lof -noLof -cancer -csvStats snpeff_stats.csv -s snpeff_stats.html kp_mero /corral4/main/objects/b/1/7/dataset_b172e50b-6552-49ca-9fe2-9a761dad0c42.dat
snpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
Usage: snpEff [eff] [options] genome_version [input_file]
variants_file : Default is STDIN
Options:
-chr <string> : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1'). Only on TXT output.
-classic : Use old style annotations instead of Sequence Ontology and Hgvs.
-csvStats <file> : Create CSV summary file.
-download : Download reference genome if not available. Default: true
-i <format> : Input format [ vcf, bed ]. Default: VCF.
-fileList : Input actually contains a list of files to process.
-o <format> : Ouput format [ vcf, gatk, bed, bedAnn ]. Default: VCF.
-s , -stats, -htmlStats : Create HTML summary file. Default is 'snpEff_summary.html'
-noStats : Do not create stats (summary) file
Results filter options:
-fi , -filterInterval <file> : Only analyze changes that intersect with the intervals specified in this file (you may use this option many times)
-no-downstream : Do not show DOWNSTREAM changes
-no-intergenic : Do not show INTERGENIC changes
-no-intron : Do not show INTRON changes
-no-upstream : Do not show UPSTREAM changes
-no-utr : Do not show 5_PRIME_UTR or 3_PRIME_UTR changes
-no <effectType> : Do not show 'EffectType'. This option can be used several times.
Annotations options:
-cancer : Perform 'cancer' comparisons (Somatic vs Germline). Default: true
-cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples.
-fastaProt <file> : Create an output file containing the resulting protein sequences.
-formatEff : Use 'EFF' field compatible with older versions (instead of 'ANN').
-geneId : Use gene ID instead of gene name (VCF output). Default: true
-hgvs : Use HGVS annotations for amino acid sub-field. Default: false
-hgvsOld : Use old HGVS notation. Default: true
-hgvs1LetterAa : Use one letter Amino acid codes in HGVS notation. Default: true
-hgvsTrId : Use transcript ID in HGVS notation. Default: true
-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.
-noHgvs : Do not add HGVS annotations.
-noLof |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/170/72170350/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/170/72170350/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Cauris_B11220.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/179/72179902/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/179/72179902/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Enterococcus.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72179907/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72179907/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Enterococcus.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72180012/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72180012/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Enterococcus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Enterococcus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72180012/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Enterococcus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72180012/working/snpeff_output/Enterococcus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72180012/working/snpeff_output/Enterococcus/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/72180012/working/snpeff_output/genomes/Enterococcus.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/72180012/working/snpeff_output/Enterococcus/sequences.fa'
00:00:01 Reading sequence 'NZ_CP038996.1', length: 2796178
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'NZ_CP038997.1', length: 123020
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'reference sequence' file: ,
Chromosome names missing in 'genes' file : 'NZ_CP038996.1''NZ_CP038997.1' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72188529/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72188529/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Enterococcus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Enterococcus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72188529/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Enterococcus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72188529/working/snpeff_output/Enterococcus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72188529/working/snpeff_output/Enterococcus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-C7N87_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-C7N87_RS00005' for NZ_PVQG01000001.1 Protein Homology CDS 0 813 -
dbxref : GenBank:WP_106001105.1
gbkey : CDS
id : cds-WP_106001105.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_708776.1
locus_tag : C7N87_RS00005
name : WP_106001105.1
parent : gene-C7N87_RS00005
partial : true
product : DUF4942 domain-containing protein
protein_id : WP_106001105.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72188529/working/snpeff_output/Enterococcus/genes.gff' line 12 'NZ_PVQG01000001.1 Protein Homology CDS 1 814 . - 0 ID=cds-WP_106001105.1;Parent=gene-C7N87_RS00005;Dbxref=GenBank:WP_106001105.1;Name=WP_106001105.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_708776.1;locus_tag=C7N87_RS00005;partial=true;product=DUF4942 domain-containing protein;protein_id=WP_106001105.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-C7N87_RS05085' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-C7N87_RS05085' for NZ_PVQG01000010.1 Protein Homology CDS 1013 1510 +
dbxref : GenBank:WP_023156898.1
gbkey : CDS
go_process : DNA replication|0006260||IEA,plasmid maintenance|0006276||IEA
id : cds-WP_023156898.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_001027759.1
locus_tag : C7N87_RS05085
name : WP_023156898.1
ontology_term : GO:0006260,GO:0006276
parent : gene-C7N87_RS05085
product : replication/maintenance protein RepL
protein_id : WP_023156898.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72188529/working/snpeff_output/Enterococcus/genes.gff' line 17 'NZ_PVQG01000010.1 Protein Homology CDS 1014 1511 . + 0 ID=cds-WP_023156898.1;Parent=gene-C7N87_RS05085;Dbxref=GenBank:WP_023156898.1;Name=WP_023156898.1;Ontology_term=GO:0006260,GO:0006276;gbkey=CDS;go_process=DNA replication|0006260||IEA,plasmid maintenance|0006276||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_001027759.1;locus_tag=C7N87_RS05085;product=replication/maintenance protein RepL;protein_id=WP_023156898.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-C7N87_RS05090' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-C7N87_RS05090' for NZ_PVQG01000010.1 Protein Homology CDS 1544 1969 -
dbxref : GenBank:WP_024257935.1
gbkey : CDS
gene : mobA
go_process : regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_024257935.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_001107325.1
locus_tag : C7N87_RS05090
name : WP_024257935.1
ontology_term : GO:0006355
parent : gene-C7N87_RS05090
product : plasmid mobilization protein MobA
protein_id : WP_024257935.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/je |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/189/72189442/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/189/72189442/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: '__tc__'
00:00:00 Reading config file: /corral4/main/jobs/072/189/72189442/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: '__tc__.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/189/72189511/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/189/72189511/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'WBcel235.86'
00:00:00 Reading config file: /corral4/main/jobs/072/189/72189511/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'WBcel235.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72197356/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72197356/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'WBcel235.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72197372/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72197372/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'WBcel235.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/205/72205358/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/205/72205358/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GR38.86'
00:00:00 Reading config file: /corral4/main/jobs/072/205/72205358/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GR38.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/210/72210511/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/210/72210511/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Snapbean_Phytozome.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/210/72210768/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/210/72210768/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Snapbean_Phytozome.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/211/72211384/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/211/72211384/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Snapbean_Phytozome.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217858/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217858/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Camp'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Camp'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72217858/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Camp'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72217858/working/snpeff_output/Camp/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72217858/working/snpeff_output/Camp/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217858/working/snpeff_output/Camp/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217858/working/snpeff_output/Camp/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/m |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217859/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217859/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Camp'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Camp'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72217859/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Camp'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72217859/working/snpeff_output/Camp/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72217859/working/snpeff_output/Camp/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217859/working/snpeff_output/Camp/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217859/working/snpeff_output/Camp/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/m |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217860/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217860/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Camp'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Camp'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72217860/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Camp'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72217860/working/snpeff_output/Camp/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72217860/working/snpeff_output/Camp/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217860/working/snpeff_output/Camp/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217860/working/snpeff_output/Camp/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/m |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217861/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217861/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Camp'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Camp'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72217861/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Camp'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72217861/working/snpeff_output/Camp/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72217861/working/snpeff_output/Camp/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217861/working/snpeff_output/Camp/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217861/working/snpeff_output/Camp/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/m |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217862/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72217862/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Camp'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Camp'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72217862/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Camp'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72217862/working/snpeff_output/Camp/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72217862/working/snpeff_output/Camp/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217862/working/snpeff_output/Camp/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72217862/working/snpeff_output/Camp/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/m |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230411/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230411/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230411/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230411/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230411/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230411/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230411/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230412/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230412/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230412/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230412/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230412/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230412/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230412/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230413/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230413/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230413/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230413/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230413/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230413/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230413/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230414/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230414/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230414/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230414/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230414/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230414/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230414/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230415/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230415/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230415/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230415/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230415/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230415/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230415/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230416/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230416/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230416/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230416/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230416/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230416/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230416/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230417/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230417/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230417/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230417/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230417/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230417/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230417/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230418/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230418/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230418/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230418/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230418/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230418/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230418/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230419/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230419/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230419/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230419/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230419/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230419/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230419/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230420/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230420/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230420/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230420/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230420/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230420/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230420/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230421/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230421/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230421/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230421/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230421/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230421/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230421/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230422/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230422/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230422/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230422/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230422/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230422/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230422/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230423/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230423/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230423/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230423/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230423/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230423/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230423/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230424/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230424/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230424/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230424/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230424/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230424/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230424/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230425/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230425/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230425/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230425/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230425/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230425/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230425/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230426/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230426/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230426/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230426/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230426/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230426/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230426/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230427/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230427/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230427/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230427/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230427/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230427/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230427/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230428/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230428/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230428/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230428/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230428/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230428/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230428/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230429/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230429/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230429/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230429/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230429/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230429/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230429/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230430/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230430/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230430/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230430/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230430/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230430/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230430/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230431/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230431/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230431/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230431/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230431/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230431/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230431/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230432/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230432/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230432/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230432/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230432/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230432/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230432/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230433/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230433/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230433/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230433/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230433/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230433/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230433/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230434/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230434/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230434/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230434/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230434/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230434/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230434/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230435/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230435/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230435/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230435/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230435/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230435/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230435/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230436/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230436/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230436/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230436/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230436/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230436/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230436/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230437/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230437/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230437/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230437/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230437/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230437/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230437/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230438/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230438/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230438/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230438/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230438/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230438/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230438/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230439/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230439/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230439/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230439/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230439/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230439/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230439/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230440/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230440/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230440/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230440/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230440/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230440/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230440/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230441/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230441/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230441/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230441/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230441/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230441/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230441/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230442/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230442/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230442/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230442/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230442/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230442/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230442/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230443/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230443/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230443/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230443/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230443/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230443/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230443/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230444/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230444/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230444/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230444/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230444/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230444/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230444/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230445/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230445/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230445/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230445/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230445/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230445/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230445/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230446/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230446/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230446/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230446/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230446/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230446/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230446/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230447/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230447/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230447/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230447/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230447/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230447/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230447/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230448/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230448/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230448/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230448/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230448/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230448/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230448/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230449/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230449/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230449/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230449/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230449/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230449/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230449/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230450/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230450/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230450/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230450/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230450/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230450/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230450/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230451/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230451/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230451/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230451/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230451/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230451/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230451/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230452/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230452/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230452/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230452/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230452/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230452/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230452/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230453/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230453/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230453/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230453/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230453/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230453/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230453/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230454/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230454/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230454/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230454/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230454/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230454/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230454/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230455/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230455/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230455/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230455/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230455/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230455/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230455/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230456/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230456/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230456/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230456/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230456/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230456/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230456/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230457/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230457/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230457/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230457/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230457/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230457/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230457/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230458/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230458/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230458/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230458/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230458/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230458/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230458/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230459/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230459/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230459/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230459/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230459/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230459/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230459/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230460/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230460/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230460/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230460/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230460/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230460/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230460/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230461/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230461/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230461/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230461/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230461/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230461/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230461/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230462/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230462/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230462/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230462/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230462/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230462/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230462/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230463/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230463/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230463/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230463/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230463/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230463/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230463/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230464/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230464/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230464/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230464/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230464/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230464/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230464/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230465/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230465/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230465/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230465/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230465/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230465/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230465/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230466/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230466/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230466/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230466/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230466/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230466/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230466/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230467/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230467/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230467/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230467/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230467/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230467/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230467/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230468/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230468/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230468/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230468/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230468/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230468/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230468/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230469/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230469/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230469/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230469/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230469/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230469/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230469/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230470/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230470/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230470/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230470/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230470/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230470/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230470/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230471/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230471/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230471/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230471/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230471/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230471/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230471/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230472/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230472/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230472/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230472/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230472/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230472/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230472/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230473/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230473/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230473/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230473/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230473/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230473/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230473/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230474/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230474/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230474/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230474/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230474/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230474/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230474/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230475/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230475/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230475/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230475/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230475/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230475/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230475/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230476/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230476/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230476/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230476/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230476/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230476/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230476/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230477/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230477/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230477/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230477/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230477/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230477/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230477/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230478/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230478/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230478/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230478/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230478/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230478/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230478/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230479/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230479/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230479/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230479/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230479/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230479/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230479/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230480/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230480/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230480/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230480/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230480/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230480/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230480/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230481/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230481/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230481/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230481/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230481/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230481/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230481/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230482/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230482/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230482/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230482/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230482/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230482/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230482/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230483/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230483/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230483/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230483/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230483/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230483/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230483/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230484/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230484/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230484/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230484/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230484/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230484/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230484/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230485/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230485/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230485/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230485/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230485/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230485/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230485/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230486/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230486/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230486/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230486/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230486/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230486/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230486/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230487/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230487/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230487/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230487/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230487/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230487/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230487/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230488/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230488/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230488/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230488/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230488/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230488/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230488/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230489/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230489/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230489/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230489/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230489/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230489/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230489/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230490/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230490/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230490/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230490/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230490/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230490/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230490/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230491/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230491/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230491/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230491/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230491/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230491/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230491/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230492/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230492/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230492/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230492/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230492/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230492/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230492/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230493/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230493/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230493/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230493/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230493/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230493/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230493/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230494/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230494/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230494/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230494/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230494/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230494/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230494/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230495/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230495/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230495/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230495/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230495/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230495/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230495/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230496/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230496/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230496/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230496/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230496/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230496/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230496/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230497/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230497/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230497/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230497/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230497/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230497/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230497/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230498/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230498/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230498/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230498/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230498/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230498/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230498/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230499/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230499/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230499/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230499/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230499/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230499/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230499/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230500/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230500/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230500/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230500/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230500/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230500/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230500/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230501/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230501/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230501/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230501/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230501/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230501/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230501/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230502/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230502/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230502/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230502/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230502/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230502/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230502/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230503/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230503/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230503/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230503/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230503/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230503/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230503/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230504/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230504/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230504/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230504/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230504/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230504/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230504/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230505/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230505/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230505/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230505/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230505/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230505/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230505/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230506/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230506/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230506/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230506/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230506/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230506/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230506/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230507/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230507/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230507/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230507/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230507/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230507/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230507/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230508/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230508/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230508/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230508/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230508/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230508/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230508/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230509/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230509/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230509/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230509/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230509/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230509/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230509/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230510/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230510/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230510/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230510/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230510/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230510/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230510/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230511/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230511/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230511/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230511/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230511/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230511/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230511/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230512/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230512/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230512/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230512/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230512/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230512/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230512/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230513/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230513/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230513/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230513/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230513/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230513/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230513/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230514/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230514/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230514/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230514/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230514/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230514/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230514/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230515/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230515/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230515/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230515/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230515/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230515/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230515/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230516/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230516/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230516/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230516/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230516/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230516/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230516/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230517/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230517/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230517/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230517/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230517/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230517/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230517/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230518/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230518/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230518/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230518/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230518/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230518/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230518/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230519/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230519/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230519/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230519/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230519/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230519/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230519/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230520/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230520/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230520/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230520/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230520/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230520/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230520/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230521/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230521/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230521/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230521/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230521/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230521/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230521/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230522/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230522/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230522/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230522/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230522/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230522/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230522/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230523/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230523/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230523/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230523/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230523/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230523/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230523/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230524/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230524/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230524/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230524/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230524/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230524/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230524/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230525/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230525/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230525/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230525/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230525/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230525/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230525/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230526/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230526/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230526/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230526/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230526/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230526/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230526/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230527/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230527/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230527/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230527/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230527/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230527/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230527/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230528/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230528/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230528/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230528/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230528/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230528/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230528/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230529/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230529/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230529/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230529/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230529/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230529/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230529/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230530/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230530/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230530/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230530/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230530/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230530/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230530/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230531/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230531/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230531/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230531/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230531/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230531/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230531/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230532/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230532/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230532/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230532/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230532/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230532/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230532/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230533/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230533/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230533/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230533/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230533/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230533/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230533/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230534/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230534/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230534/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230534/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230534/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230534/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230534/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230535/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230535/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230535/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230535/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230535/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230535/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230535/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230536/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230536/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230536/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230536/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230536/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230536/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230536/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230537/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230537/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230537/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230537/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230537/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230537/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230537/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230538/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230538/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230538/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230538/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230538/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230538/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230538/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230539/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230539/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230539/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230539/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230539/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230539/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230539/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230540/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230540/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230540/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230540/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230540/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230540/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230540/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230541/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230541/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230541/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230541/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230541/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230541/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230541/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230542/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230542/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230542/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230542/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230542/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230542/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230542/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230543/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230543/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230543/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230543/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230543/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230543/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230543/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230544/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230544/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230544/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230544/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230544/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230544/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230544/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230545/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230545/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230545/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230545/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230545/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230545/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230545/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230546/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230546/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230546/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230546/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230546/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230546/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230546/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230547/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230547/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230547/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230547/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230547/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230547/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230547/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230548/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230548/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230548/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230548/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230548/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230548/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230548/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230549/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230549/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230549/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230549/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230549/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230549/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230549/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230550/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230550/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230550/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230550/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230550/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230550/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230550/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230551/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230551/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230551/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230551/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230551/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230551/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230551/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230552/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230552/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230552/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230552/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230552/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230552/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230552/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230553/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230553/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230553/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230553/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230553/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230553/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230553/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230554/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230554/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230554/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230554/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230554/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230554/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230554/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230555/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230555/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230555/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230555/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230555/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230555/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230555/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230556/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230556/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230556/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230556/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230556/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230556/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230556/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230557/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230557/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230557/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230557/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230557/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230557/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230557/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230558/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230558/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230558/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230558/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230558/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230558/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230558/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230559/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230559/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230559/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230559/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230559/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230559/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230559/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230560/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230560/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230560/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230560/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230560/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230560/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230560/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230561/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230561/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230561/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230561/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230561/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230561/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230561/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230562/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230562/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230562/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230562/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230562/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230562/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230562/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230563/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230563/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230563/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230563/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230563/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230563/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230563/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230564/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230564/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230564/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230564/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230564/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230564/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230564/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230565/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230565/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230565/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230565/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230565/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230565/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230565/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230566/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230566/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230566/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230566/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230566/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230566/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230566/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230567/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230567/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230567/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230567/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230567/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230567/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230567/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230568/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230568/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230568/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230568/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230568/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230568/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230568/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230569/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230569/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230569/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230569/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230569/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230569/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230569/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230570/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230570/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230570/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230570/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230570/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230570/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230570/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230571/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230571/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230571/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230571/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230571/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230571/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230571/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230572/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230572/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230572/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230572/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230572/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230572/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230572/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230573/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230573/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230573/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230573/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230573/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230573/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230573/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230574/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230574/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230574/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230574/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230574/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230574/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230574/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230575/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230575/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230575/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230575/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230575/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230575/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230575/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230576/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230576/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230576/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230576/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230576/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230576/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230576/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230577/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230577/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230577/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230577/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230577/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230577/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230577/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230578/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230578/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230578/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230578/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230578/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230578/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230578/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230579/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230579/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230579/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230579/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230579/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230579/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230579/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230580/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230580/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230580/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230580/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230580/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230580/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230580/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230581/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230581/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230581/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230581/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230581/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230581/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230581/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230582/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230582/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230582/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230582/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230582/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230582/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230582/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230583/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230583/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230583/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230583/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230583/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230583/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230583/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230584/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230584/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230584/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230584/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230584/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230584/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230584/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230585/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230585/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230585/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230585/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230585/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230585/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230585/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230586/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230586/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230586/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230586/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230586/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230586/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230586/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230587/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230587/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230587/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230587/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230587/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230587/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230587/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230588/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230588/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230588/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230588/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230588/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230588/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230588/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230589/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230589/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230589/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230589/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230589/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230589/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230589/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230590/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230590/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230590/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230590/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230590/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230590/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230590/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230591/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230591/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230591/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230591/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230591/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230591/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230591/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230592/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230592/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230592/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230592/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230592/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230592/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230592/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230593/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230593/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230593/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230593/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230593/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230593/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230593/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230594/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230594/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230594/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230594/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230594/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230594/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230594/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230595/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230595/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230595/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230595/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230595/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230595/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230595/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230596/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230596/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230596/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230596/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230596/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230596/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230596/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230597/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230597/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230597/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230597/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230597/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230597/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230597/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230598/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230598/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230598/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230598/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230598/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230598/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230598/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230599/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230599/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230599/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230599/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230599/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230599/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230599/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230600/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230600/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230600/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230600/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230600/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230600/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230600/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230601/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230601/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230601/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230601/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230601/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230601/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230601/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230602/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230602/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230602/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230602/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230602/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230602/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230602/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230603/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230603/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230603/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230603/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230603/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230603/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230603/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230604/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230604/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230604/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230604/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230604/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230604/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230604/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230605/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230605/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230605/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230605/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230605/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230605/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230605/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230606/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230606/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230606/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230606/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230606/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230606/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230606/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230607/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230607/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230607/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230607/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230607/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230607/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230607/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230608/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230608/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230608/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230608/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230608/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230608/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230608/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230609/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230609/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230609/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230609/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230609/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230609/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230609/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230610/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230610/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230610/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230610/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230610/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230610/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230610/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230611/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230611/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230611/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230611/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230611/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230611/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230611/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230612/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72230612/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'cc'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'cc'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72230612/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'cc'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72230612/working/snpeff_output/cc/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72230612/working/snpeff_output/cc/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00010' for NZ_CP046317.1 Protein Homology CDS 928 2451 -
dbxref : GenBank:WP_002779494.1,GeneID:66543518
gbkey : CDS
gene : dcuC
go_component : membrane|0016020||IEA
go_function : C4-dicarboxylate transmembrane transporter activity|0015556||IEA
go_process : C4-dicarboxylate transport|0015740||IEA
id : cds-WP_002779494.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1
locus_tag : FOC43_RS00010
name : WP_002779494.1
ontology_term : GO:0015740,GO:0015556,GO:0016020
parent : gene-FOC43_RS00010
product : C4-dicarboxylate transporter DcuC
protein_id : WP_002779494.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230612/working/snpeff_output/cc/genes.gff' line 12 'NZ_CP046317.1 Protein Homology CDS 929 2452 . - 0 ID=cds-WP_002779494.1;Parent=gene-FOC43_RS00010;Dbxref=GenBank:WP_002779494.1,GeneID:66543518;Name=WP_002779494.1;Ontology_term=GO:0015740,GO:0015556,GO:0016020;gbkey=CDS;gene=dcuC;go_component=membrane|0016020||IEA;go_function=C4-dicarboxylate transmembrane transporter activity|0015556||IEA;go_process=C4-dicarboxylate transport|0015740||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002831351.1;locus_tag=FOC43_RS00010;product=C4-dicarboxylate transporter DcuC;protein_id=WP_002779494.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00015' for NZ_CP046317.1 GeneMarkS-2+ CDS 2761 3063 +
dbxref : GenBank:WP_002779493.1,GeneID:66543519
gbkey : CDS
id : cds-WP_002779493.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : FOC43_RS00015
name : WP_002779493.1
parent : gene-FOC43_RS00015
product : hypothetical protein
protein_id : WP_002779493.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230612/working/snpeff_output/cc/genes.gff' line 14 'NZ_CP046317.1 GeneMarkS-2+ CDS 2762 3064 . + 0 ID=cds-WP_002779493.1;Parent=gene-FOC43_RS00015;Dbxref=GenBank:WP_002779493.1,GeneID:66543519;Name=WP_002779493.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=FOC43_RS00015;product=hypothetical protein;protein_id=WP_002779493.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-FOC43_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-FOC43_RS00020' for NZ_CP046317.1 Protein Homology CDS 3119 3556 +
dbxref : GenBank:WP_002779492.1,GeneID:66543520
gbkey : CDS
id : cds-WP_002779492.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002779492.1
locus_tag : FOC43_RS00020
name : WP_002779492.1
parent : gene-FOC43_RS00020
product : hypothetical protein
protein_id : WP_002779492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72230 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/235/72235727/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/235/72235727/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: '40: SnpEff eff: on dataset 39'
00:00:00 Reading config file: /corral4/main/jobs/072/235/72235727/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: '40: SnpEff eff: on dataset 39.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/235/72235780/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/235/72235780/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/235/72235780/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/236/72236666/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/236/72236666/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'ZIKA.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/248/72248004/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/248/72248004/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'kp_mero'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/8/b/0/dataset_8b03809e-05a4-4154-b6b2-1093d054b586.dat' (line: 1):
CP003200.1 0 5333942 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/252/72252799/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/252/72252799/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Snapbean2.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72253332/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72253332/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'WBcel235.105.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1000)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/254/72254102/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/254/72254102/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Snap.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/255/72255226/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/255/72255226/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg19: Homo_sapiens (UCSC)'
00:00:00 Reading config file: /corral4/main/jobs/072/255/72255226/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'hg19: Homo_sapiens (UCSC).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/255/72255267/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/255/72255267/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'grc37.75.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/255/72255494/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/255/72255494/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'WBcel235.105.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1000)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/259/72259419/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/259/72259419/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg19 database'
00:00:00 Reading config file: /corral4/main/jobs/072/259/72259419/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'hg19 database.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/263/72263890/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/263/72263890/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCF_000001405.40.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/266/72266405/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/266/72266405/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.86'
00:00:00 Reading config file: /corral4/main/jobs/072/266/72266405/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
00:00:02 done
00:00:02 Downloading database for 'GRCh38.86'
00:00:02 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_GRCh38.86.zip' to local file '/corral4/main/jobs/072/266/72266405/tmp/snpEff_v5_2_GRCh38.86.zip'
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_GRCh38.86.zip
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_GRCh38.86.zip, using proxy: false
00:00:03 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_GRCh38.86.zip
00:00:03 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_GRCh38.86.zip' to local file '/corral4/main/jobs/072/266/72266405/tmp/snpEff_v5_0_GRCh38.86.zip'
00:00:03 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_GRCh38.86.zip
00:00:03 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_GRCh38.86.zip, using proxy: false
00:00:03 Local file name: '/corral4/main/jobs/072/266/72266405/tmp/snpEff_v5_0_GRCh38.86.zip'
..........00:00:04 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_GRCh38.86.zip
00:00:04 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_GRCh38.86.zip' to local file '/corral4/main/jobs/072/266/72266405/tmp/snpEff_v5_1_GRCh38.86.zip'
00:00:04 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_GRCh38.86.zip
00:00:04 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_GRCh38.86.zip, using proxy: false
00:00:04 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_GRCh38.86.zip
FATAL ERROR: Failed to download database from [https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_GRCh38.86.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_GRCh38.86.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_GRCh38.86.zip] |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/266/72266450/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/266/72266450/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.86, mm10'
00:00:00 Reading config file: /corral4/main/jobs/072/266/72266450/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.86, mm10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269010/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269010/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269010/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269010/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269010/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269010/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269010/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269010/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269011/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269011/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269011/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269011/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269011/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269011/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269011/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269011/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269012/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269012/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269012/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269012/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269012/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269012/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269012/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269012/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269013/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269013/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269013/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269013/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269013/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269013/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269013/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269013/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269014/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269014/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269014/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269014/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269014/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269014/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269014/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269014/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269015/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269015/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269015/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269015/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269015/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269015/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269015/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269015/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269016/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269016/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269016/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269016/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269016/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269016/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269016/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269016/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269017/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269017/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269017/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269017/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269017/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269017/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269017/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269017/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269018/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269018/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269018/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269018/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269018/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269018/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269018/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269018/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269019/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269019/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269019/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269019/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269019/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269019/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269019/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269019/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269020/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269020/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269020/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269020/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269020/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269020/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269020/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269020/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269021/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269021/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269021/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269021/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269021/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269021/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269021/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269021/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269022/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269022/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269022/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269022/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269022/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269022/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269022/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269022/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269023/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269023/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269023/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269023/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269023/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269023/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269023/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269023/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269024/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269024/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269024/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269024/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269024/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269024/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269024/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269024/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269025/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269025/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269025/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269025/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269025/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269025/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269025/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269025/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269026/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269026/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269026/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269026/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269026/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269026/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269026/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269026/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269027/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269027/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269027/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269027/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269027/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269027/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269027/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269027/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269028/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269028/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269028/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269028/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269028/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269028/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269028/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269028/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269029/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269029/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269029/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269029/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269029/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269029/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269029/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269029/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269030/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269030/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269030/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269030/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269030/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269030/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269030/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269030/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269031/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269031/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269031/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269031/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269031/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269031/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269031/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269031/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269032/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269032/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269032/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269032/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269032/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269032/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269032/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269032/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269033/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269033/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269033/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269033/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269033/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269033/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269033/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269033/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269034/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269034/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269034/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269034/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269034/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269034/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269034/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269034/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269035/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269035/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269035/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269035/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269035/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269035/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269035/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269035/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269036/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269036/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269036/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269036/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269036/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269036/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269036/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269036/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269037/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269037/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269037/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269037/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269037/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269037/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269037/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269037/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269038/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269038/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269038/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269038/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269038/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269038/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269038/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269038/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269039/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269039/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269039/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269039/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269039/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269039/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269039/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269039/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269040/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269040/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269040/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269040/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269040/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269040/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269040/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269040/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269041/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269041/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269041/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269041/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269041/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269041/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269041/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269041/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269042/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269042/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269042/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269042/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269042/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269042/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269042/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269042/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269043/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269043/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269043/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269043/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269043/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269043/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269043/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269043/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269044/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269044/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269044/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269044/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269044/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269044/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269044/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269044/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269045/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269045/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269045/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269045/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269045/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269045/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269045/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269045/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269046/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269046/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269046/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269046/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269046/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269046/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269046/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269046/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269047/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269047/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269047/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269047/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269047/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269047/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269047/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269047/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269048/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269048/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269048/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269048/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269048/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269048/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269048/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269048/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269049/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269049/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269049/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269049/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269049/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269049/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269049/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269049/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269050/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269050/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269050/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269050/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269050/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269050/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269050/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269050/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269051/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269051/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269051/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269051/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269051/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269051/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269051/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269051/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269052/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269052/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269052/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269052/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269052/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269052/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269052/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269052/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269053/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269053/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269053/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269053/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269053/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269053/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269053/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269053/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269054/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269054/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269054/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269054/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269054/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269054/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269054/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269054/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269055/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269055/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269055/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269055/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269055/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269055/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269055/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269055/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269056/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269056/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269056/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269056/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269056/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269056/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269056/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269056/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269057/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269057/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269057/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269057/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269057/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269057/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269057/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269057/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269058/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269058/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269058/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269058/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269058/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269058/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269058/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269058/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269059/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269059/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269059/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269059/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269059/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269059/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269059/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269059/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269060/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269060/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269060/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269060/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269060/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269060/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269060/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269060/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269061/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269061/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269061/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269061/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269061/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269061/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269061/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269061/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269062/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269062/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269062/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269062/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269062/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269062/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269062/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269062/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269063/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269063/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269063/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269063/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269063/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269063/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269063/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269063/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269064/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269064/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269064/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269064/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269064/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269064/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269064/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269064/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269065/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269065/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269065/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269065/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269065/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269065/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269065/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269065/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269066/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269066/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269066/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269066/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269066/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269066/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269066/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269066/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269067/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269067/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269067/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269067/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269067/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269067/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269067/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269067/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269068/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269068/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269068/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269068/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269068/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269068/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269068/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269068/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269069/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269069/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269069/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269069/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269069/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269069/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269069/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269069/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269070/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269070/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269070/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269070/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269070/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269070/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269070/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269070/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269071/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269071/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269071/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269071/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269071/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269071/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269071/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269071/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269072/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269072/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269072/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269072/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269072/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269072/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269072/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269072/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269073/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269073/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269073/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269073/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269073/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269073/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269073/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269073/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269074/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269074/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269074/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269074/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269074/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269074/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269074/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269074/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269075/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269075/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269075/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269075/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269075/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269075/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269075/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269075/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269076/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269076/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269076/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269076/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269076/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269076/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269076/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269076/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269077/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269077/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269077/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269077/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269077/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269077/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269077/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269077/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269078/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269078/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269078/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269078/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269078/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269078/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269078/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269078/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269079/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269079/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269079/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269079/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269079/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269079/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269079/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269079/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269080/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269080/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269080/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269080/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269080/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269080/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269080/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269080/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269081/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269081/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269081/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269081/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269081/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269081/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269081/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269081/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269082/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269082/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269082/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269082/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269082/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269082/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269082/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269082/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269083/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269083/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269083/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269083/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269083/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269083/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269083/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269083/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269084/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269084/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269084/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269084/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269084/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269084/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269084/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269084/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269085/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269085/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269085/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269085/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269085/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269085/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269085/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269085/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269086/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269086/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269086/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269086/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269086/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269086/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269086/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269086/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269087/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269087/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269087/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269087/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269087/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269087/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269087/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269087/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269088/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269088/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269088/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269088/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269088/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269088/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269088/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269088/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269089/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269089/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269089/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269089/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269089/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269089/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269089/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269089/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269090/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269090/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269090/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269090/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269090/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269090/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269090/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269090/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269091/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269091/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269091/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269091/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269091/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269091/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269091/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269091/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269092/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269092/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269092/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269092/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269092/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269092/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269092/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269092/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269093/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269093/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269093/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269093/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269093/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269093/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269093/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269093/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269094/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269094/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269094/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269094/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269094/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269094/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269094/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269094/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269095/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269095/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269095/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269095/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269095/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269095/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269095/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269095/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269096/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269096/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269096/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269096/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269096/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269096/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269096/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269096/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269097/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269097/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269097/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269097/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269097/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269097/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269097/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269097/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269098/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269098/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269098/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269098/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269098/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269098/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269098/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269098/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269099/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269099/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269099/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269099/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269099/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269099/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269099/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269099/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269100/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269100/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269100/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269100/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269100/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269100/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269100/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269100/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269101/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269101/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269101/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269101/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269101/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269101/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269101/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269101/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269102/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269102/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269102/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269102/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269102/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269102/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269102/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269102/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269103/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269103/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269103/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269103/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269103/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269103/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269103/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269103/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269104/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269104/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269104/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269104/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269104/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269104/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269104/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269104/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269105/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269105/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269105/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269105/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269105/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269105/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269105/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269105/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269106/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269106/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269106/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269106/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269106/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269106/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269106/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269106/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269107/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269107/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269107/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269107/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269107/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269107/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269107/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269107/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269108/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269108/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269108/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269108/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269108/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269108/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269108/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269108/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269109/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269109/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269109/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269109/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269109/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269109/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269109/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269109/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269110/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269110/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269110/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269110/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269110/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269110/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269110/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269110/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269111/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269111/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269111/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269111/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269111/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269111/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269111/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269111/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269112/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269112/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269112/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269112/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269112/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269112/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269112/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269112/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269113/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269113/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269113/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269113/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269113/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269113/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269113/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269113/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269114/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269114/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269114/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269114/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269114/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269114/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269114/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269114/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269115/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269115/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269115/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269115/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269115/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269115/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269115/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269115/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269116/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269116/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269116/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269116/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269116/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269116/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269116/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269116/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269117/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269117/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269117/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269117/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269117/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269117/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269117/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269117/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269118/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269118/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269118/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269118/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269118/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269118/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269118/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269118/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269119/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269119/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269119/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269119/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269119/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269119/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269119/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269119/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269120/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269120/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269120/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269120/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269120/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269120/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269120/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269120/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269121/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269121/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269121/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269121/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269121/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269121/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269121/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269121/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269122/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269122/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269122/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269122/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269122/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269122/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269122/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269122/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269123/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269123/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269123/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269123/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269123/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269123/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269123/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269123/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269124/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269124/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269124/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269124/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269124/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269124/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269124/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269124/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269125/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269125/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269125/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269125/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269125/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269125/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269125/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269125/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269126/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269126/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269126/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269126/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269126/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269126/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269126/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269126/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269127/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269127/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269127/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269127/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269127/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269127/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269127/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269127/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269128/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269128/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269128/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269128/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269128/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269128/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269128/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269128/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269129/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269129/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269129/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269129/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269129/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269129/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269129/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269129/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269130/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269130/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269130/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269130/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269130/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269130/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269130/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269130/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269131/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269131/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269131/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269131/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269131/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269131/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269131/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269131/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269132/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269132/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269132/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269132/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269132/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269132/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269132/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269132/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269133/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269133/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269133/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269133/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269133/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269133/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269133/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269133/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269134/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269134/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269134/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269134/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269134/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269134/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269134/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269134/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269135/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269135/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269135/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269135/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269135/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269135/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269135/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269135/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269136/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269136/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269136/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269136/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269136/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269136/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269136/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269136/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269137/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269137/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269137/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269137/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269137/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269137/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269137/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269137/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269138/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269138/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269138/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269138/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269138/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269138/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269138/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269138/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269139/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269139/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269139/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269139/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269139/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269139/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269139/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269139/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269140/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269140/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269140/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269140/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269140/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269140/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269140/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269140/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269141/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269141/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269141/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269141/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269141/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269141/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269141/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269141/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269142/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269142/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269142/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269142/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269142/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269142/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269142/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269142/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269143/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269143/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269143/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269143/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269143/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269143/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269143/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269143/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269144/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269144/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269144/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269144/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269144/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269144/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269144/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269144/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269145/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269145/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269145/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269145/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269145/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269145/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269145/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269145/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269146/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269146/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269146/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269146/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269146/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269146/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269146/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269146/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269147/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269147/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269147/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269147/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269147/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269147/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269147/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269147/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269148/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269148/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269148/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269148/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269148/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269148/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269148/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269148/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269149/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269149/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269149/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269149/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269149/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269149/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269149/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269149/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269150/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269150/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269150/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269150/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269150/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269150/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269150/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269150/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269151/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269151/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269151/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269151/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269151/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269151/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269151/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269151/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269152/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269152/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269152/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269152/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269152/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269152/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269152/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269152/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269153/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269153/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269153/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269153/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269153/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269153/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269153/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269153/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269154/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269154/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269154/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269154/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269154/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269154/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269154/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269154/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269155/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269155/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269155/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269155/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269155/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269155/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269155/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269155/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269156/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269156/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269156/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269156/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269156/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269156/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269156/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269156/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269157/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269157/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269157/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269157/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269157/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269157/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269157/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269157/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269158/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269158/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269158/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269158/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269158/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269158/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269158/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269158/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269159/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269159/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269159/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269159/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269159/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269159/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269159/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269159/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269160/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269160/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269160/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269160/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269160/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269160/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269160/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269160/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269161/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269161/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269161/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269161/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269161/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269161/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269161/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269161/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269162/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269162/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269162/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269162/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269162/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269162/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269162/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269162/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269163/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269163/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269163/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269163/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269163/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269163/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269163/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269163/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269164/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269164/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269164/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269164/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269164/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269164/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269164/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269164/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269165/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269165/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269165/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269165/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269165/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269165/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269165/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269165/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269166/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269166/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269166/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269166/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269166/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269166/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269166/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269166/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269167/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269167/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269167/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269167/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269167/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269167/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269167/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269167/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269168/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269168/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269168/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269168/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269168/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269168/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269168/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269168/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269169/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269169/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269169/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269169/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269169/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269169/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269169/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269169/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269170/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269170/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269170/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269170/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269170/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269170/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269170/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269170/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269171/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269171/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269171/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269171/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269171/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269171/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269171/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269171/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269172/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269172/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269172/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269172/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269172/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269172/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269172/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269172/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269173/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269173/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269173/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269173/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269173/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269173/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269173/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269173/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269174/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269174/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269174/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269174/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269174/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269174/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269174/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269174/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269175/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269175/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269175/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269175/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269175/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269175/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269175/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269175/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269176/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269176/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269176/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269176/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269176/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269176/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269176/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269176/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269177/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269177/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269177/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269177/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269177/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269177/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269177/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269177/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269178/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269178/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269178/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269178/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269178/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269178/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269178/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269178/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269179/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269179/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269179/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269179/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269179/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269179/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269179/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269179/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269180/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269180/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269180/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269180/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269180/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269180/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269180/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269180/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269181/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269181/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269181/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269181/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269181/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269181/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269181/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269181/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269182/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269182/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269182/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269182/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269182/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269182/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269182/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269182/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269183/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269183/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269183/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269183/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269183/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269183/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269183/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269183/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269184/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269184/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269184/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269184/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269184/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269184/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269184/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269184/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269185/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269185/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269185/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269185/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269185/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269185/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269185/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269185/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269186/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269186/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269186/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269186/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269186/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269186/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269186/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269186/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269187/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269187/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269187/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269187/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269187/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269187/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269187/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269187/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269188/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269188/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269188/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269188/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269188/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269188/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269188/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269188/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269189/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269189/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269189/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269189/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269189/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269189/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269189/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269189/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269190/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269190/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269190/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269190/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269190/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269190/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269190/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269190/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269191/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269191/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269191/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269191/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269191/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269191/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269191/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269191/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269192/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269192/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269192/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269192/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269192/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269192/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269192/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269192/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269193/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269193/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269193/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269193/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269193/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269193/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269193/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269193/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269194/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269194/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269194/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269194/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269194/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269194/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269194/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269194/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269195/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269195/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269195/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269195/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269195/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269195/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269195/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269195/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269196/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269196/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269196/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269196/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269196/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269196/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269196/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269196/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269197/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269197/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269197/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269197/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269197/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269197/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269197/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269197/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269198/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269198/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269198/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269198/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269198/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269198/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269198/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269198/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269199/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269199/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269199/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269199/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269199/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269199/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269199/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269199/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269200/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269200/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269200/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269200/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269200/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269200/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269200/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269200/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269201/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269201/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269201/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269201/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269201/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269201/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269201/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269201/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269202/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269202/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269202/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269202/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269202/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269202/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269202/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269202/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269203/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269203/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269203/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269203/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269203/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269203/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269203/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269203/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269204/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269204/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269204/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269204/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269204/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269204/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269204/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269204/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269205/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269205/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269205/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269205/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269205/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269205/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269205/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269205/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269206/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269206/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269206/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269206/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269206/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269206/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269206/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269206/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269207/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269207/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269207/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269207/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269207/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269207/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269207/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269207/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269208/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269208/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269208/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269208/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269208/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269208/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269208/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269208/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269209/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269209/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269209/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269209/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269209/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269209/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269209/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269209/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269210/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269210/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269210/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269210/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269210/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269210/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269210/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269210/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269211/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269211/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269211/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269211/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269211/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269211/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269211/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269211/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269212/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269212/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269212/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269212/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269212/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269212/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269212/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269212/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269213/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269213/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269213/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269213/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269213/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269213/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269213/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269213/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269214/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269214/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269214/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269214/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269214/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269214/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269214/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269214/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269215/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269215/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269215/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269215/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269215/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269215/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269215/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269215/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269216/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269216/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269216/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269216/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269216/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269216/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269216/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269216/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269217/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269217/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269217/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269217/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269217/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269217/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269217/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269217/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269218/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269218/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269218/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269218/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269218/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269218/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269218/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269218/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269219/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269219/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269219/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269219/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269219/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269219/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269219/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269219/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269220/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269220/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269220/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269220/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269220/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269220/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269220/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269220/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269221/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269221/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269221/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269221/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269221/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269221/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269221/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269221/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269222/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269222/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269222/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269222/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269222/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269222/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269222/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269222/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269223/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269223/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269223/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269223/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269223/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269223/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269223/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269223/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269224/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269224/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269224/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269224/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269224/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269224/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269224/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269224/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269225/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269225/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269225/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269225/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269225/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269225/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269225/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269225/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269226/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269226/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269226/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269226/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269226/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269226/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269226/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269226/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269227/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269227/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269227/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269227/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269227/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269227/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269227/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269227/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269228/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269228/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269228/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269228/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269228/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269228/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269228/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269228/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269229/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269229/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269229/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269229/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269229/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269229/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269229/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269229/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269230/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269230/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269230/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269230/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269230/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269230/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269230/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269230/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269231/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269231/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269231/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269231/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269231/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269231/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269231/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269231/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269232/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269232/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269232/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269232/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269232/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269232/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269232/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269232/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269233/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269233/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269233/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269233/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269233/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269233/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269233/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269233/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269234/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269234/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269234/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269234/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269234/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269234/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269234/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269234/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269235/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269235/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269235/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269235/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269235/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269235/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269235/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269235/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269236/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269236/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269236/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269236/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269236/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269236/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269236/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269236/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269237/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269237/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269237/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269237/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269237/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269237/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269237/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269237/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269238/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269238/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269238/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269238/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269238/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269238/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269238/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269238/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269239/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269239/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269239/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269239/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269239/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269239/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269239/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269239/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269240/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269240/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269240/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269240/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269240/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269240/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269240/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269240/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269241/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269241/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269241/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269241/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269241/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269241/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269241/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269241/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269242/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269242/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269242/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269242/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269242/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269242/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269242/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269242/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269243/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269243/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269243/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269243/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269243/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269243/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269243/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269243/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269244/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269244/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269244/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269244/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269244/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269244/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269244/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269244/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269245/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269245/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269245/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269245/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269245/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269245/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269245/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269245/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269246/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269246/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269246/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269246/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269246/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269246/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269246/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269246/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269247/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269247/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269247/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269247/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269247/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269247/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269247/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269247/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269248/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269248/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269248/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269248/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269248/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269248/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269248/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269248/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269249/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269249/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269249/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269249/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269249/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269249/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269249/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269249/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269250/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269250/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269250/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269250/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269250/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269250/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269250/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269250/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269251/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269251/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269251/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269251/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269251/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269251/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269251/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269251/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269252/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269252/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269252/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269252/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269252/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269252/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269252/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269252/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269253/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269253/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269253/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269253/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269253/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269253/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269253/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269253/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269254/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269254/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269254/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269254/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269254/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269254/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269254/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269254/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269255/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269255/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269255/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269255/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269255/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269255/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269255/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269255/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269256/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269256/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269256/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269256/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269256/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269256/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269256/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269256/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269257/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269257/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269257/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269257/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269257/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269257/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269257/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269257/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269258/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269258/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269258/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269258/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269258/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269258/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269258/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269258/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269259/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269259/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269259/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269259/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269259/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269259/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269259/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269259/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269260/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269260/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269260/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269260/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269260/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269260/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269260/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269260/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269261/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269261/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269261/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269261/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269261/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269261/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269261/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269261/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269262/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269262/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269262/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269262/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269262/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269262/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269262/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269262/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269263/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269263/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269263/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269263/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269263/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269263/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269263/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269263/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269264/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269264/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269264/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269264/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269264/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269264/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269264/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269264/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269265/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269265/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269265/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269265/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269265/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269265/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269265/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269265/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269266/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269266/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269266/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269266/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269266/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269266/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269266/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269266/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269267/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269267/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269267/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269267/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269267/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269267/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269267/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269267/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269268/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269268/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269268/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269268/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269268/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269268/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269268/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269268/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269269/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269269/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269269/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269269/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269269/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269269/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269269/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269269/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269270/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269270/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269270/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269270/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269270/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269270/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269270/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269270/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269271/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269271/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269271/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269271/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269271/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269271/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269271/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269271/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269272/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269272/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269272/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269272/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269272/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269272/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269272/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269272/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269273/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269273/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269273/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269273/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269273/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269273/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269273/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269273/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269274/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269274/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269274/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269274/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269274/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269274/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269274/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269274/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269275/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269275/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269275/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269275/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269275/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269275/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269275/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269275/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269276/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269276/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269276/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269276/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269276/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269276/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269276/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269276/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269277/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269277/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269277/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269277/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269277/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269277/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269277/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269277/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269278/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269278/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269278/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269278/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269278/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269278/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269278/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269278/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269279/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269279/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269279/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269279/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269279/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269279/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269279/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269279/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269280/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269280/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269280/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269280/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269280/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269280/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269280/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269280/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269281/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269281/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269281/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269281/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269281/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269281/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269281/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269281/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269282/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269282/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269282/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269282/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269282/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269282/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269282/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269282/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269283/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269283/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269283/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269283/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269283/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269283/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269283/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269283/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269284/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269284/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269284/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269284/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269284/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269284/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269284/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269284/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269285/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269285/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269285/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269285/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269285/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269285/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269285/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269285/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269286/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269286/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269286/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269286/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269286/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269286/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269286/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269286/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269287/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269287/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269287/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269287/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269287/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269287/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269287/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269287/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269288/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269288/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269288/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269288/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269288/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269288/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269288/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269288/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269289/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269289/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269289/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269289/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269289/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269289/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269289/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269289/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269290/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269290/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269290/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269290/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269290/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269290/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269290/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269290/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269291/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269291/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269291/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269291/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269291/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269291/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269291/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269291/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269292/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269292/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269292/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269292/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269292/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269292/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269292/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269292/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269293/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269293/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269293/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269293/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269293/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269293/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269293/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269293/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269294/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269294/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269294/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269294/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269294/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269294/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269294/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269294/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269295/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269295/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269295/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269295/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269295/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269295/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269295/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269295/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269296/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269296/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269296/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269296/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269296/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269296/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269296/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269296/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269297/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269297/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269297/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269297/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269297/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269297/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269297/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269297/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269298/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269298/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269298/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269298/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269298/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269298/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269298/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269298/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269299/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269299/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269299/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269299/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269299/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269299/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269299/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269299/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269300/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269300/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269300/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269300/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269300/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269300/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269300/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269300/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269301/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269301/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269301/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269301/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269301/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269301/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269301/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269301/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269302/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269302/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269302/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269302/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269302/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269302/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269302/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269302/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269303/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269303/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269303/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269303/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269303/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269303/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269303/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269303/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269304/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269304/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269304/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269304/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269304/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269304/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269304/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269304/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269305/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269305/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269305/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269305/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269305/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269305/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269305/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269305/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269306/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269306/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269306/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269306/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269306/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269306/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269306/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269306/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269307/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269307/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269307/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269307/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269307/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269307/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269307/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269307/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269308/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269308/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269308/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269308/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269308/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269308/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269308/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269308/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269309/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269309/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269309/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269309/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269309/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269309/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269309/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269309/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269310/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269310/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269310/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269310/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269310/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269310/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269310/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269310/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269311/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269311/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269311/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269311/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269311/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269311/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269311/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269311/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269312/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269312/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269312/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269312/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269312/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269312/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269312/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269312/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269313/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269313/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269313/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269313/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269313/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269313/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269313/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269313/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269314/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269314/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269314/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269314/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269314/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269314/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269314/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269314/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269315/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269315/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269315/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269315/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269315/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269315/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269315/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269315/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269316/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269316/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269316/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269316/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269316/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269316/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269316/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269316/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269317/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269317/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269317/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269317/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269317/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269317/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269317/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269317/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269318/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269318/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269318/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269318/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269318/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269318/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269318/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269318/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269319/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269319/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269319/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269319/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269319/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269319/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269319/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269319/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269320/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269320/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269320/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269320/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269320/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269320/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269320/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269320/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269321/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269321/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269321/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269321/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269321/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269321/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269321/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269321/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269322/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269322/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269322/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269322/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269322/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269322/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269322/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269322/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269323/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269323/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269323/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269323/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269323/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269323/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269323/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269323/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269324/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269324/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269324/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269324/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269324/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269324/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269324/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269324/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269325/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269325/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269325/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269325/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269325/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269325/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269325/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269325/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269326/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269326/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269326/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269326/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269326/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269326/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269326/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269326/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269327/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269327/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269327/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269327/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269327/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269327/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269327/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269327/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269328/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269328/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269328/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269328/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269328/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269328/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269328/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269328/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269329/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269329/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269329/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269329/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269329/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269329/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269329/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269329/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269330/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269330/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269330/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269330/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269330/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269330/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269330/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269330/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269331/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269331/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269331/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269331/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269331/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269331/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269331/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269331/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269332/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269332/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269332/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269332/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269332/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269332/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269332/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269332/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269333/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269333/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269333/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269333/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269333/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269333/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269333/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269333/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269334/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269334/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269334/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269334/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269334/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269334/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269334/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269334/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269335/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269335/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269335/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269335/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269335/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269335/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269335/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269335/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269336/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269336/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269336/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269336/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269336/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269336/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269336/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269336/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269337/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269337/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269337/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269337/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269337/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269337/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269337/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269337/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269338/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269338/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269338/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269338/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269338/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269338/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269338/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269338/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269339/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269339/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269339/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269339/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269339/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269339/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269339/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269339/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269340/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269340/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269340/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269340/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269340/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269340/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269340/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269340/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269341/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269341/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269341/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269341/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269341/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269341/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269341/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269341/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269342/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269342/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269342/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269342/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269342/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269342/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269342/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269342/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269343/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269343/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269343/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269343/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269343/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269343/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269343/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269343/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269344/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269344/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269344/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269344/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269344/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269344/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269344/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269344/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269345/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269345/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269345/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269345/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269345/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269345/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269345/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269345/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269346/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269346/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269346/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269346/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269346/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269346/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269346/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269346/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269347/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269347/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269347/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269347/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269347/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269347/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269347/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269347/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269348/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269348/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269348/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269348/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269348/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269348/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269348/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269348/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269349/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269349/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269349/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269349/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269349/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269349/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269349/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269349/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269350/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269350/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269350/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269350/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269350/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269350/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269350/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269350/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269351/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269351/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269351/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269351/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269351/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269351/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269351/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269351/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269352/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269352/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269352/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269352/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269352/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269352/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269352/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269352/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269353/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269353/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269353/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269353/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269353/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269353/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269353/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269353/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269354/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269354/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269354/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269354/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269354/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269354/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269354/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269354/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269355/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269355/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269355/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269355/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269355/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269355/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269355/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269355/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269356/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269356/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269356/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269356/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269356/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269356/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269356/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269356/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269357/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269357/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269357/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269357/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269357/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269357/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269357/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269357/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269358/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269358/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269358/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269358/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269358/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269358/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269358/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269358/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269359/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269359/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269359/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269359/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269359/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269359/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269359/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269359/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269360/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269360/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269360/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269360/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269360/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269360/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269360/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269360/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269361/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269361/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269361/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269361/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269361/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269361/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269361/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269361/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269362/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269362/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269362/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269362/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269362/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269362/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269362/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269362/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269363/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269363/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269363/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269363/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269363/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269363/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269363/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269363/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269364/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269364/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269364/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269364/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269364/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269364/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269364/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269364/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269365/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269365/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269365/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269365/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269365/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269365/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269365/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269365/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269366/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269366/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269366/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269366/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269366/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269366/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269366/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269366/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269367/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269367/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269367/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269367/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269367/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269367/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269367/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269367/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269368/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269368/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269368/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269368/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269368/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269368/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269368/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269368/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269369/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269369/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269369/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269369/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269369/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269369/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269369/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269369/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269370/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269370/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269370/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269370/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269370/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269370/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269370/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269370/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269371/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269371/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269371/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269371/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269371/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269371/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269371/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269371/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269372/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269372/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269372/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269372/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269372/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269372/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269372/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269372/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269373/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269373/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269373/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269373/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269373/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269373/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269373/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269373/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269374/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269374/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269374/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269374/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269374/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269374/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269374/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269374/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269375/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269375/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269375/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269375/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269375/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269375/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269375/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269375/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269376/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269376/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269376/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269376/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269376/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269376/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269376/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269376/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269377/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269377/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269377/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269377/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269377/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269377/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269377/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269377/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269378/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269378/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269378/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269378/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269378/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269378/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269378/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269378/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269379/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269379/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269379/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269379/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269379/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269379/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269379/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269379/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269380/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269380/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269380/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269380/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269380/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269380/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269380/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269380/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269381/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269381/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269381/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269381/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269381/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269381/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269381/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269381/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269382/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269382/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269382/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269382/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269382/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269382/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269382/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269382/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269383/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269383/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269383/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269383/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269383/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269383/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269383/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269383/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269384/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269384/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269384/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269384/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269384/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269384/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269384/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269384/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269385/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269385/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269385/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269385/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269385/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269385/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269385/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269385/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269386/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269386/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269386/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269386/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269386/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269386/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269386/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269386/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269387/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269387/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269387/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269387/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269387/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269387/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269387/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269387/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269388/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269388/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269388/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269388/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269388/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269388/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269388/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269388/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269389/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269389/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269389/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269389/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269389/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269389/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269389/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269389/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269390/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269390/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269390/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269390/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269390/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269390/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269390/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269390/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269391/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269391/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269391/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269391/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269391/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269391/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269391/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269391/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269392/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269392/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269392/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269392/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269392/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269392/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269392/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269392/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269393/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269393/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269393/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269393/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269393/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269393/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269393/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269393/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269394/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269394/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269394/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269394/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269394/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269394/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269394/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269394/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269395/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269395/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269395/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269395/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269395/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269395/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269395/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269395/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269396/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269396/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269396/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269396/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269396/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269396/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269396/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269396/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269397/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269397/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269397/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269397/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269397/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269397/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269397/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269397/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269398/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269398/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269398/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269398/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269398/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269398/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269398/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269398/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269399/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269399/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269399/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269399/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269399/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269399/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269399/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269399/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269400/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269400/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269400/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269400/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269400/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269400/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269400/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269400/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269401/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269401/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269401/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269401/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269401/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269401/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269401/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269401/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269402/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269402/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269402/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269402/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269402/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269402/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269402/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269402/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269403/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269403/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269403/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269403/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269403/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269403/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269403/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269403/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269404/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269404/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269404/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269404/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269404/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269404/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269404/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269404/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269405/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269405/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269405/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269405/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269405/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269405/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269405/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269405/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269406/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269406/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269406/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269406/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269406/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269406/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269406/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269406/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269407/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269407/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269407/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269407/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269407/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269407/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269407/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269407/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269408/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269408/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269408/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269408/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269408/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269408/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269408/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269408/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269409/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72269409/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72269409/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72269409/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72269409/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269409/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269409/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72269409/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/270/72270389/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/270/72270389/tmp -Xmx11059m -Xms256m
FATAL ERROR: No transcripts left for analysis after filter using file '/corral4/main/objects/d/6/6/dataset_d6694010-0a9d-4b61-9d52-11f6f016f975.dat' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271735/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271735/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271735/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271735/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271735/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY962_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY962_RS00005' for NZ_RXUH01000001.1 Protein Homology CDS 35 523 -
dbxref : GenBank:WP_003123955.1
gbkey : CDS
gene : phzB
id : cds-WP_003123955.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252900.1
locus_tag : DY962_RS00005
name : WP_003123955.1
parent : gene-DY962_RS00005
product : phenazine biosynthesis protein PhzB
protein_id : WP_003123955.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271735/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUH01000001.1 Protein Homology CDS 36 524 . - 0 ID=cds-WP_003123955.1;Parent=gene-DY962_RS00005;Dbxref=GenBank:WP_003123955.1;Name=WP_003123955.1;gbkey=CDS;gene=phzB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252900.1;locus_tag=DY962_RS00005;product=phenazine biosynthesis protein PhzB;protein_id=WP_003123955.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY962_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY962_RS00010' for NZ_RXUH01000001.1 Protein Homology CDS 553 1041 -
dbxref : GenBank:WP_003114729.1
gbkey : CDS
gene : phzA
id : cds-WP_003114729.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252899.1
locus_tag : DY962_RS00010
name : WP_003114729.1
parent : gene-DY962_RS00010
product : phenazine biosynthesis protein PhzA
protein_id : WP_003114729.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271735/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUH01000001.1 Protein Homology CDS 554 1042 . - 0 ID=cds-WP_003114729.1;Parent=gene-DY962_RS00010;Dbxref=GenBank:WP_003114729.1;Name=WP_003114729.1;gbkey=CDS;gene=phzA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252899.1;locus_tag=DY962_RS00010;product=phenazine biosynthesis protein PhzA;protein_id=WP_003114729.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY962_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY962_RS00020' for NZ_RXUH01000001.1 Protein Homology CDS 1738 2742 +
dbxref : GenBank:WP_003093617.1
gbkey : CDS
gene : phzM
id : cds-WP_003093617.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252898.1
locus_tag : DY962_RS00020
name : WP_003093617.1
parent : gene-DY962_RS00020
product : phenazine-1-carboxylate N-methyltransferase PhzM
protein_id : WP_003093617.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271735/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUH01000001.1 Protein Homology CDS 1739 2743 . + 0 ID=cds-WP_003093617.1;Parent=gene-DY962_RS00020;Dbxref=GenBank:WP_003093617.1;Name=WP_003093617.1;gbkey=CDS;gene=phzM;infe |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271736/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271736/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271736/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271736/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271736/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY973_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY973_RS00005' for NZ_RXUS01000001.1 Protein Homology CDS 131 1456 -
dbxref : GenBank:WP_019484535.1
gbkey : CDS
id : cds-WP_019484535.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_019726828.1
locus_tag : DY973_RS00005
name : WP_019484535.1
parent : gene-DY973_RS00005
product : STY4528 family pathogenicity island replication protein
protein_id : WP_019484535.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271736/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUS01000001.1 Protein Homology CDS 132 1457 . - 0 ID=cds-WP_019484535.1;Parent=gene-DY973_RS00005;Dbxref=GenBank:WP_019484535.1;Name=WP_019484535.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_019726828.1;locus_tag=DY973_RS00005;product=STY4528 family pathogenicity island replication protein;protein_id=WP_019484535.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY973_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY973_RS00010' for NZ_RXUS01000001.1 Protein Homology CDS 1453 2220 -
dbxref : GenBank:WP_004352844.1
gbkey : CDS
id : cds-WP_004352844.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003157035.1
locus_tag : DY973_RS00010
name : WP_004352844.1
parent : gene-DY973_RS00010
product : DUF2857 domain-containing protein
protein_id : WP_004352844.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271736/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUS01000001.1 Protein Homology CDS 1454 2221 . - 0 ID=cds-WP_004352844.1;Parent=gene-DY973_RS00010;Dbxref=GenBank:WP_004352844.1;Name=WP_004352844.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003157035.1;locus_tag=DY973_RS00010;product=DUF2857 domain-containing protein;protein_id=WP_004352844.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY973_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY973_RS00015' for NZ_RXUS01000001.1 Protein Homology CDS 2248 3981 -
dbxref : GenBank:WP_019484534.1
gbkey : CDS
id : cds-WP_019484534.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003158178.1
locus_tag : DY973_RS00015
name : WP_019484534.1
parent : gene-DY973_RS00015
product : ParB family protein
protein_id : WP_019484534.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271736/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUS01000001.1 Protein Homology CDS 2249 3982 . - 0 ID=cds-WP_019484534.1;Parent=gene-DY973_RS00015;Dbxref=GenBank:WP_019484534.1;Name=WP_019484534.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271737/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271737/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271737/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271737/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271737/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY985_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY985_RS00005' for NZ_RXVG01000001.1 Protein Homology CDS 324 3419 -
dbxref : GenBank:WP_016561550.1
gbkey : CDS
gene : dnaE2
id : cds-WP_016561550.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY985_RS00005
name : WP_016561550.1
parent : gene-DY985_RS00005
product : error-prone DNA polymerase
protein_id : WP_016561550.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271737/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVG01000001.1 Protein Homology CDS 325 3420 . - 0 ID=cds-WP_016561550.1;Parent=gene-DY985_RS00005;Dbxref=GenBank:WP_016561550.1;Name=WP_016561550.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY985_RS00005;product=error-prone DNA polymerase;protein_id=WP_016561550.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY985_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY985_RS00010' for NZ_RXVG01000001.1 Protein Homology CDS 3395 4810 -
dbxref : GenBank:WP_023084699.1
gbkey : CDS
id : cds-WP_023084699.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY985_RS00010
name : WP_023084699.1
parent : gene-DY985_RS00010
product : Y-family DNA polymerase
protein_id : WP_023084699.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271737/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVG01000001.1 Protein Homology CDS 3396 4811 . - 0 ID=cds-WP_023084699.1;Parent=gene-DY985_RS00010;Dbxref=GenBank:WP_023084699.1;Name=WP_023084699.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY985_RS00010;product=Y-family DNA polymerase;protein_id=WP_023084699.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY985_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY985_RS00015' for NZ_RXVG01000001.1 Protein Homology CDS 4818 5423 -
dbxref : GenBank:WP_031627677.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031627677.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003296675.1
locus_tag : DY985_RS00015
name : WP_031627677.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY985_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031627677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271737/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVG01000001.1 Protein Homology CDS 4819 5424 . - 0 ID=cds-WP_031627677.1;Parent=gene-DY985_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271738/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271738/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271738/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271738/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271738/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY957_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY957_RS00010' for NZ_RXUC01000001.1 Protein Homology CDS 584 2113 +
dbxref : GenBank:WP_003097684.1
gbkey : CDS
gene : nuoM
go_function : NADH dehydrogenase (ubiquinone) activity|0008137||IEA
go_process : ATP synthesis coupled electron transport|0042773||IEA
id : cds-WP_003097684.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251338.1
locus_tag : DY957_RS00010
name : WP_003097684.1
ontology_term : GO:0042773,GO:0008137
parent : gene-DY957_RS00010
product : NADH-quinone oxidoreductase subunit M
protein_id : WP_003097684.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271738/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUC01000001.1 Protein Homology CDS 585 2114 . + 0 ID=cds-WP_003097684.1;Parent=gene-DY957_RS00010;Dbxref=GenBank:WP_003097684.1;Name=WP_003097684.1;Ontology_term=GO:0042773,GO:0008137;gbkey=CDS;gene=nuoM;go_function=NADH dehydrogenase (ubiquinone) activity|0008137||IEA;go_process=ATP synthesis coupled electron transport|0042773||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251338.1;locus_tag=DY957_RS00010;product=NADH-quinone oxidoreductase subunit M;protein_id=WP_003097684.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY957_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY957_RS00015' for NZ_RXUC01000001.1 Protein Homology CDS 2121 3581 +
dbxref : GenBank:WP_003090482.1
gbkey : CDS
gene : nuoN
go_function : NADH dehydrogenase (ubiquinone) activity|0008137||IEA
id : cds-WP_003090482.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251339.1
locus_tag : DY957_RS00015
name : WP_003090482.1
ontology_term : GO:0008137
parent : gene-DY957_RS00015
product : NADH-quinone oxidoreductase subunit NuoN
protein_id : WP_003090482.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271738/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUC01000001.1 Protein Homology CDS 2122 3582 . + 0 ID=cds-WP_003090482.1;Parent=gene-DY957_RS00015;Dbxref=GenBank:WP_003090482.1;Name=WP_003090482.1;Ontology_term=GO:0008137;gbkey=CDS;gene=nuoN;go_function=NADH dehydrogenase (ubiquinone) activity|0008137||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251339.1;locus_tag=DY957_RS00015;product=NADH-quinone oxidoreductase subunit NuoN;protein_id=WP_003090482.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY957_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY957_RS00020' for NZ_RXUC01000001.1 Protein Homology CDS 3696 4505 +
dbxref : GenBank:WP_003138925.1
gbkey : CDS
go_function : methyltransferase activity|0008168||IEA,S-adenosyl-L-me |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271739/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271739/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271739/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271739/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271739/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA19_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA19_RS00010' for NZ_RXWO01000001.1 Protein Homology CDS 274 1980 +
dbxref : GenBank:WP_003449760.1
gbkey : CDS
id : cds-WP_003449760.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250201.1
locus_tag : DZA19_RS00010
name : WP_003449760.1
parent : gene-DZA19_RS00010
product : esterase/lipase family protein
protein_id : WP_003449760.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271739/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWO01000001.1 Protein Homology CDS 275 1981 . + 0 ID=cds-WP_003449760.1;Parent=gene-DZA19_RS00010;Dbxref=GenBank:WP_003449760.1;Name=WP_003449760.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250201.1;locus_tag=DZA19_RS00010;product=esterase/lipase family protein;protein_id=WP_003449760.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA19_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA19_RS00015' for NZ_RXWO01000001.1 Protein Homology CDS 1977 3122 +
dbxref : GenBank:WP_031633157.1
gbkey : CDS
id : cds-WP_031633157.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003083213.1
locus_tag : DZA19_RS00015
name : WP_031633157.1
parent : gene-DZA19_RS00015
product : T6SS immunity protein Tli4 family protein
protein_id : WP_031633157.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271739/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWO01000001.1 Protein Homology CDS 1978 3123 . + 0 ID=cds-WP_031633157.1;Parent=gene-DZA19_RS00015;Dbxref=GenBank:WP_031633157.1;Name=WP_031633157.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003083213.1;locus_tag=DZA19_RS00015;product=T6SS immunity protein Tli4 family protein;protein_id=WP_031633157.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA19_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA19_RS00020' for NZ_RXWO01000001.1 Protein Homology CDS 3135 3395 +
dbxref : GenBank:WP_003083211.1
gbkey : CDS
id : cds-WP_003083211.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250199.1
locus_tag : DZA19_RS00020
name : WP_003083211.1
parent : gene-DZA19_RS00020
product : PAAR domain-containing protein
protein_id : WP_003083211.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271739/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXWO01000001.1 Protein Homology CDS 3136 3396 . + 0 ID=cds-WP_003083211.1;Parent=gene-DZA19_RS00020;Dbxref=GenBank:WP_003083211.1;Name=WP_003083211.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250199.1;locus_tag=DZ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271740/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271740/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271740/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271740/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271740/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA16_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA16_RS00010' for NZ_RXWL01000001.1 Protein Homology CDS 255 1964 +
dbxref : GenBank:WP_003118705.1
gbkey : CDS
id : cds-WP_003118705.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250201.1
locus_tag : DZA16_RS00010
name : WP_003118705.1
parent : gene-DZA16_RS00010
product : esterase/lipase family protein
protein_id : WP_003118705.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271740/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWL01000001.1 Protein Homology CDS 256 1965 . + 0 ID=cds-WP_003118705.1;Parent=gene-DZA16_RS00010;Dbxref=GenBank:WP_003118705.1;Name=WP_003118705.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250201.1;locus_tag=DZA16_RS00010;product=esterase/lipase family protein;protein_id=WP_003118705.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA16_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA16_RS00015' for NZ_RXWL01000001.1 Protein Homology CDS 1961 3103 +
dbxref : GenBank:WP_003118704.1
gbkey : CDS
id : cds-WP_003118704.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250200.1
locus_tag : DZA16_RS00015
name : WP_003118704.1
parent : gene-DZA16_RS00015
product : T6SS immunity protein Tli4 family protein
protein_id : WP_003118704.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271740/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWL01000001.1 Protein Homology CDS 1962 3104 . + 0 ID=cds-WP_003118704.1;Parent=gene-DZA16_RS00015;Dbxref=GenBank:WP_003118704.1;Name=WP_003118704.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250200.1;locus_tag=DZA16_RS00015;product=T6SS immunity protein Tli4 family protein;protein_id=WP_003118704.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA16_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA16_RS00020' for NZ_RXWL01000001.1 Protein Homology CDS 3116 3376 +
dbxref : GenBank:WP_003083211.1
gbkey : CDS
id : cds-WP_003083211.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250199.1
locus_tag : DZA16_RS00020
name : WP_003083211.1
parent : gene-DZA16_RS00020
product : PAAR domain-containing protein
protein_id : WP_003083211.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271740/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXWL01000001.1 Protein Homology CDS 3117 3377 . + 0 ID=cds-WP_003083211.1;Parent=gene-DZA16_RS00020;Dbxref=GenBank:WP_003083211.1;Name=WP_003083211.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250199.1;locus_tag=DZA16_RS |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271741/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271741/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271741/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271741/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271741/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA11_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA11_RS00005' for NZ_RXWG01000001.1 Protein Homology CDS 101 2005 -
dbxref : GenBank:WP_003103223.1
gbkey : CDS
go_function : metallocarboxypeptidase activity|0004181||IEA,zinc ion binding|0008270||IEA
go_process : proteolysis|0006508||IEA
id : cds-WP_003103223.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251744.1
locus_tag : DZA11_RS00005
name : WP_003103223.1
ontology_term : GO:0006508,GO:0004181,GO:0008270
parent : gene-DZA11_RS00005
product : M14 family metallopeptidase
protein_id : WP_003103223.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271741/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWG01000001.1 Protein Homology CDS 102 2006 . - 0 ID=cds-WP_003103223.1;Parent=gene-DZA11_RS00005;Dbxref=GenBank:WP_003103223.1;Name=WP_003103223.1;Ontology_term=GO:0006508,GO:0004181,GO:0008270;gbkey=CDS;go_function=metallocarboxypeptidase activity|0004181||IEA,zinc ion binding|0008270||IEA;go_process=proteolysis|0006508||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251744.1;locus_tag=DZA11_RS00005;product=M14 family metallopeptidase;protein_id=WP_003103223.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA11_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA11_RS00010' for NZ_RXWG01000001.1 Protein Homology CDS 2173 3174 -
dbxref : GenBank:WP_003103224.1
gbkey : CDS
id : cds-WP_003103224.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251743.1
locus_tag : DZA11_RS00010
name : WP_003103224.1
parent : gene-DZA11_RS00010
product : alpha/beta fold hydrolase
protein_id : WP_003103224.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271741/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWG01000001.1 Protein Homology CDS 2174 3175 . - 0 ID=cds-WP_003103224.1;Parent=gene-DZA11_RS00010;Dbxref=GenBank:WP_003103224.1;Name=WP_003103224.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251743.1;locus_tag=DZA11_RS00010;product=alpha/beta fold hydrolase;protein_id=WP_003103224.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA11_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA11_RS00015' for NZ_RXWG01000001.1 Protein Homology CDS 3246 4127 -
dbxref : GenBank:WP_023086048.1
gbkey : CDS
id : cds-WP_023086048.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012075108.1
locus_tag : DZA11_RS00015
name : WP_023086048.1
parent : gene-DZA11_RS00015
product : DUF6685 family protein
protein_id : WP_023086048.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271741/wor |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271742/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271742/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271742/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271742/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271742/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY990_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY990_RS00005' for NZ_RXVL01000001.1 Protein Homology CDS 143 751 -
dbxref : GenBank:WP_016253925.1
gbkey : CDS
gene : msrQ
id : cds-WP_016253925.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253379.1
locus_tag : DY990_RS00005
name : WP_016253925.1
parent : gene-DY990_RS00005
product : protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
protein_id : WP_016253925.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271742/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVL01000001.1 Protein Homology CDS 144 752 . - 0 ID=cds-WP_016253925.1;Parent=gene-DY990_RS00005;Dbxref=GenBank:WP_016253925.1;Name=WP_016253925.1;gbkey=CDS;gene=msrQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253379.1;locus_tag=DY990_RS00005;product=protein-methionine-sulfoxide reductase heme-binding subunit MsrQ;protein_id=WP_016253925.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY990_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY990_RS00010' for NZ_RXVL01000001.1 Protein Homology CDS 751 1764 -
dbxref : GenBank:WP_031755652.1
gbkey : CDS
gene : msrP
go_function : oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA
go_process : protein repair|0030091||IEA
id : cds-WP_031755652.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253380.1
locus_tag : DY990_RS00010
name : WP_031755652.1
ontology_term : GO:0030091,GO:0016667,GO:0043546
parent : gene-DY990_RS00010
product : protein-methionine-sulfoxide reductase catalytic subunit MsrP
protein_id : WP_031755652.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271742/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVL01000001.1 Protein Homology CDS 752 1765 . - 0 ID=cds-WP_031755652.1;Parent=gene-DY990_RS00010;Dbxref=GenBank:WP_031755652.1;Name=WP_031755652.1;Ontology_term=GO:0030091,GO:0016667,GO:0043546;gbkey=CDS;gene=msrP;go_function=oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA;go_process=protein repair|0030091||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253380.1;locus_tag=DY990_RS00010;product=protein-methionine-sulfoxide reductase catalytic subunit MsrP;protein_id=WP_031755652.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY990_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY990_RS00015' for NZ_RXVL01000001.1 Protein Homology CDS 1825 2640 -
dbxref : GenBank:WP_003095061.1
gbkey : CDS
gene : pssA
go_function : CDP-diacylglycerol-serine O-phosph |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271743/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271743/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271743/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271743/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271743/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA14_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA14_RS00005' for NZ_RXWJ01000001.1 Protein Homology CDS 80 961 +
dbxref : GenBank:WP_003141969.1
gbkey : CDS
id : cds-WP_003141969.1
inference : COORDINATES: protein motif:HMM:NF024894.5
locus_tag : DZA14_RS00005
name : WP_003141969.1
parent : gene-DZA14_RS00005
product : DUF4123 domain-containing protein
protein_id : WP_003141969.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271743/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWJ01000001.1 Protein Homology CDS 81 962 . + 0 ID=cds-WP_003141969.1;Parent=gene-DZA14_RS00005;Dbxref=GenBank:WP_003141969.1;Name=WP_003141969.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024894.5;locus_tag=DZA14_RS00005;product=DUF4123 domain-containing protein;protein_id=WP_003141969.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA14_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA14_RS00010' for NZ_RXWJ01000001.1 Protein Homology CDS 958 4482 +
dbxref : GenBank:WP_003141967.1
gbkey : CDS
id : cds-WP_003141967.1
inference : COORDINATES: protein motif:HMM:NF042700.3
locus_tag : DZA14_RS00010
name : WP_003141967.1
parent : gene-DZA14_RS00010
product : toxin VasX
protein_id : WP_003141967.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271743/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWJ01000001.1 Protein Homology CDS 959 4483 . + 0 ID=cds-WP_003141967.1;Parent=gene-DZA14_RS00010;Dbxref=GenBank:WP_003141967.1;Name=WP_003141967.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF042700.3;locus_tag=DZA14_RS00010;product=toxin VasX;protein_id=WP_003141967.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA14_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA14_RS00015' for NZ_RXWJ01000001.1 Protein Homology CDS 4535 5608 +
dbxref : GenBank:WP_003141965.1
gbkey : CDS
id : cds-WP_003141965.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003123708.1
locus_tag : DZA14_RS00015
name : WP_003141965.1
parent : gene-DZA14_RS00015
product : hypothetical protein
protein_id : WP_003141965.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271743/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWJ01000001.1 Protein Homology CDS 4536 5609 . + 0 ID=cds-WP_003141965.1;Parent=gene-DZA14_RS00015;Dbxref=GenBank:WP_003141965.1;Name=WP_003141965.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003123708.1;locus_tag=DZA14_RS00015;product=hypothetical protein;protein_id=WP_003141965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271744/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271744/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271744/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271744/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271744/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY958_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY958_RS00005' for NZ_RXUD01000001.1 Protein Homology CDS 380 1351 +
dbxref : GenBank:WP_126644202.1
gbkey : CDS
gene : pstS
id : cds-WP_126644202.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254056.1
locus_tag : DY958_RS00005
name : WP_126644202.1
parent : gene-DY958_RS00005
product : phosphate ABC transporter substrate-binding protein PstS
protein_id : WP_126644202.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271744/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUD01000001.1 Protein Homology CDS 381 1352 . + 0 ID=cds-WP_126644202.1;Parent=gene-DY958_RS00005;Dbxref=GenBank:WP_126644202.1;Name=WP_126644202.1;gbkey=CDS;gene=pstS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254056.1;locus_tag=DY958_RS00005;product=phosphate ABC transporter substrate-binding protein PstS;protein_id=WP_126644202.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY958_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY958_RS00010' for NZ_RXUD01000001.1 Protein Homology CDS 1774 3807 +
dbxref : GenBank:WP_078464131.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_078464131.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254055.1
locus_tag : DY958_RS00010
name : WP_078464131.1
ontology_term : GO:0055085,GO:0016020
parent : gene-DY958_RS00010
product : ABC transporter permease subunit
protein_id : WP_078464131.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271744/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUD01000001.1 Protein Homology CDS 1775 3808 . + 0 ID=cds-WP_078464131.1;Parent=gene-DY958_RS00010;Dbxref=GenBank:WP_078464131.1;Name=WP_078464131.1;Ontology_term=GO:0055085,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254055.1;locus_tag=DY958_RS00010;product=ABC transporter permease subunit;protein_id=WP_078464131.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY958_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY958_RS00015' for NZ_RXUD01000001.1 Protein Homology CDS 3827 5503 +
dbxref : GenBank:WP_023107420.1
gbkey : CDS
gene : pstA
go_component : plasma membrane|0005886||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ATPase-coupled phosphate ion transmembrane transporter activity|0015415||IEA
go_process : phosphate ion transport|0006817||IEA
id : cds-WP_023107420.1
inference : COORDINATES: |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271745/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271745/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271745/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271745/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271745/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA12_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA12_RS00010' for NZ_RXWH01000001.1 Protein Homology CDS 1588 1806 +
dbxref : GenBank:WP_003108468.1
gbkey : CDS
id : cds-WP_003108468.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_016264198.1
locus_tag : DZA12_RS00010
name : WP_003108468.1
parent : gene-DZA12_RS00010
product : hypothetical protein
protein_id : WP_003108468.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271745/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWH01000001.1 Protein Homology CDS 1589 1807 . + 0 ID=cds-WP_003108468.1;Parent=gene-DZA12_RS00010;Dbxref=GenBank:WP_003108468.1;Name=WP_003108468.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016264198.1;locus_tag=DZA12_RS00010;product=hypothetical protein;protein_id=WP_003108468.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA12_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA12_RS00020' for NZ_RXWH01000001.1 Protein Homology CDS 2020 2469 +
dbxref : GenBank:WP_071534877.1
gbkey : CDS
go_function : N-acetyltransferase activity|0008080||IEA,acyltransferase activity|0016746||IEA
id : cds-WP_071534877.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015503379.1
locus_tag : DZA12_RS00020
name : WP_071534877.1
ontology_term : GO:0008080,GO:0016746
parent : gene-DZA12_RS00020
product : GNAT family N-acetyltransferase
protein_id : WP_071534877.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271745/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWH01000001.1 Protein Homology CDS 2021 2470 . + 0 ID=cds-WP_071534877.1;Parent=gene-DZA12_RS00020;Dbxref=GenBank:WP_071534877.1;Name=WP_071534877.1;Ontology_term=GO:0008080,GO:0016746;gbkey=CDS;go_function=N-acetyltransferase activity|0008080||IEA,acyltransferase activity|0016746||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015503379.1;locus_tag=DZA12_RS00020;product=GNAT family N-acetyltransferase;protein_id=WP_071534877.1;transl_table=11'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_RXWH01000001.1:1804-1956) does not include 'gene-DZA12_RS00030' (NZ_RXWH01000001.1:3586-4303). Created new gene 'null.2' (NZ_RXWH01000001.1:3586-4303). File '/jetstream2/scratch/main/jobs/72271745/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 19 'NZ_RXWH01000001.1 RefSeq pseudogene 3586 4303 . + . ID=gene-DZA12_RS00030;Name=DZA12_RS00030;gbkey=Gene;gene_biotype=pseudogene;locus_tag=DZA12_RS00030;old_locus_tag=DZA12_00030;partial=true;pseudo=true;start_range=.,3586'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA12_RS00035' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA12_RS00035' for NZ_RXWH01000001.1 P |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271746/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271746/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271746/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271746/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271746/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA05_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA05_RS00005' for NZ_RXWA01000001.1 Protein Homology CDS 4 475 +
dbxref : GenBank:WP_033874414.1
end_range : 476,.
gbkey : CDS
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_033874414.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248954.1
locus_tag : DZA05_RS00005
name : WP_033874414.1
ontology_term : GO:0033103
parent : gene-DZA05_RS00005
partial : true
product : Hcp family type VI secretion system effector
protein_id : WP_033874414.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271746/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWA01000001.1 Protein Homology CDS 5 476 . + 0 ID=cds-WP_033874414.1;Parent=gene-DZA05_RS00005;Dbxref=GenBank:WP_033874414.1;Name=WP_033874414.1;Ontology_term=GO:0033103;end_range=476,.;gbkey=CDS;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248954.1;locus_tag=DZA05_RS00005;partial=true;product=Hcp family type VI secretion system effector;protein_id=WP_033874414.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA05_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA05_RS00010' for NZ_RXWA01000002.1 Protein Homology CDS 216 2291 +
dbxref : GenBank:WP_126577172.1
gbkey : CDS
go_component : type VI protein secretion system complex|0033104||IEA
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_126577172.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253953.1
locus_tag : DZA05_RS00010
name : WP_126577172.1
ontology_term : GO:0033103,GO:0033104
parent : gene-DZA05_RS00010
product : type VI secretion system tip protein VgrG
protein_id : WP_126577172.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271746/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RXWA01000002.1 Protein Homology CDS 217 2292 . + 0 ID=cds-WP_126577172.1;Parent=gene-DZA05_RS00010;Dbxref=GenBank:WP_126577172.1;Name=WP_126577172.1;Ontology_term=GO:0033103,GO:0033104;gbkey=CDS;go_component=type VI protein secretion system complex|0033104||IEA;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253953.1;locus_tag=DZA05_RS00010;product=type VI secretion system tip protein VgrG;protein_id=WP_126577172.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA05_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA05_RS00015' for NZ_RXWA01000002.1 GeneMarkS-2+ CDS 2288 5557 +
dbxref : GenBank:WP_126577173.1
|
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271747/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271747/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271747/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271747/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271747/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY997_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY997_RS00005' for NZ_RXVS01000001.1 Protein Homology CDS 294 3389 -
dbxref : GenBank:WP_126590179.1
gbkey : CDS
gene : dnaE2
id : cds-WP_126590179.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY997_RS00005
name : WP_126590179.1
parent : gene-DY997_RS00005
product : error-prone DNA polymerase
protein_id : WP_126590179.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271747/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVS01000001.1 Protein Homology CDS 295 3390 . - 0 ID=cds-WP_126590179.1;Parent=gene-DY997_RS00005;Dbxref=GenBank:WP_126590179.1;Name=WP_126590179.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY997_RS00005;product=error-prone DNA polymerase;protein_id=WP_126590179.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY997_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY997_RS00010' for NZ_RXVS01000001.1 Protein Homology CDS 3365 4780 -
dbxref : GenBank:WP_033983570.1
gbkey : CDS
id : cds-WP_033983570.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY997_RS00010
name : WP_033983570.1
parent : gene-DY997_RS00010
product : Y-family DNA polymerase
protein_id : WP_033983570.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271747/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVS01000001.1 Protein Homology CDS 3366 4781 . - 0 ID=cds-WP_033983570.1;Parent=gene-DY997_RS00010;Dbxref=GenBank:WP_033983570.1;Name=WP_033983570.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY997_RS00010;product=Y-family DNA polymerase;protein_id=WP_033983570.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY997_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY997_RS00015' for NZ_RXVS01000001.1 Protein Homology CDS 4788 5393 -
dbxref : GenBank:WP_031627677.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031627677.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003296675.1
locus_tag : DY997_RS00015
name : WP_031627677.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY997_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031627677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271747/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVS01000001.1 Protein Homology CDS 4789 5394 . - 0 ID=cds-WP_031627677.1;Parent=gene-DY997_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271748/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271748/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271748/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271748/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271748/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY969_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY969_RS00010' for NZ_RXUO01000001.1 Protein Homology CDS 255 1964 +
dbxref : GenBank:WP_003114302.1
gbkey : CDS
id : cds-WP_003114302.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250201.1
locus_tag : DY969_RS00010
name : WP_003114302.1
parent : gene-DY969_RS00010
product : esterase/lipase family protein
protein_id : WP_003114302.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271748/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUO01000001.1 Protein Homology CDS 256 1965 . + 0 ID=cds-WP_003114302.1;Parent=gene-DY969_RS00010;Dbxref=GenBank:WP_003114302.1;Name=WP_003114302.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250201.1;locus_tag=DY969_RS00010;product=esterase/lipase family protein;protein_id=WP_003114302.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY969_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY969_RS00015' for NZ_RXUO01000001.1 Protein Homology CDS 1961 3103 +
dbxref : GenBank:WP_010895573.1
gbkey : CDS
id : cds-WP_010895573.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250200.1
locus_tag : DY969_RS00015
name : WP_010895573.1
parent : gene-DY969_RS00015
product : T6SS immunity protein Tli4 family protein
protein_id : WP_010895573.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271748/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUO01000001.1 Protein Homology CDS 1962 3104 . + 0 ID=cds-WP_010895573.1;Parent=gene-DY969_RS00015;Dbxref=GenBank:WP_010895573.1;Name=WP_010895573.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250200.1;locus_tag=DY969_RS00015;product=T6SS immunity protein Tli4 family protein;protein_id=WP_010895573.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY969_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY969_RS00020' for NZ_RXUO01000001.1 Protein Homology CDS 3116 3376 +
dbxref : GenBank:WP_003083211.1
gbkey : CDS
id : cds-WP_003083211.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250199.1
locus_tag : DY969_RS00020
name : WP_003083211.1
parent : gene-DY969_RS00020
product : PAAR domain-containing protein
protein_id : WP_003083211.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271748/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXUO01000001.1 Protein Homology CDS 3117 3377 . + 0 ID=cds-WP_003083211.1;Parent=gene-DY969_RS00020;Dbxref=GenBank:WP_003083211.1;Name=WP_003083211.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250199.1;locus_tag=DY969_RS |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271749/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271749/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271749/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271749/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271749/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA04_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA04_RS00010' for NZ_RXVZ01000001.1 Protein Homology CDS 216 1067 +
dbxref : GenBank:WP_003112064.1
gbkey : CDS
id : cds-WP_003112064.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1
locus_tag : DZA04_RS00010
name : WP_003112064.1
parent : gene-DZA04_RS00010
product : D-hexose-6-phosphate mutarotase
protein_id : WP_003112064.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271749/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVZ01000001.1 Protein Homology CDS 217 1068 . + 0 ID=cds-WP_003112064.1;Parent=gene-DZA04_RS00010;Dbxref=GenBank:WP_003112064.1;Name=WP_003112064.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1;locus_tag=DZA04_RS00010;product=D-hexose-6-phosphate mutarotase;protein_id=WP_003112064.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA04_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA04_RS00015' for NZ_RXVZ01000001.1 Protein Homology CDS 1076 1933 -
dbxref : GenBank:WP_003091466.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA,carbohydrate derivative binding|0097367||IEA
go_process : DNA-templated transcription|0006351||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003091466.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251874.1
locus_tag : DZA04_RS00015
name : WP_003091466.1
ontology_term : GO:0006351,GO:0006355,GO:0003677,GO:0003700,GO:0097367
parent : gene-DZA04_RS00015
product : MurR/RpiR family transcriptional regulator
protein_id : WP_003091466.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271749/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVZ01000001.1 Protein Homology CDS 1077 1934 . - 0 ID=cds-WP_003091466.1;Parent=gene-DZA04_RS00015;Dbxref=GenBank:WP_003091466.1;Name=WP_003091466.1;Ontology_term=GO:0006351,GO:0006355,GO:0003677,GO:0003700,GO:0097367;gbkey=CDS;go_function=DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA,carbohydrate derivative binding|0097367||IEA;go_process=DNA-templated transcription|0006351||IEA,regulation of DNA-templated transcription|0006355||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251874.1;locus_tag=DZA04_RS00015;product=MurR/RpiR family transcriptional regulator;protein_id=WP_003091466.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA04_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA04_RS00020' for NZ_RXVZ01000001.1 Protein Homology CDS 2120 3589 +
dbxref : GenBank:WP_003091465.1
gbkey : CDS
gene : zwf
go_function : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271750/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271750/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271750/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271750/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271750/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY959_RS33180' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY959_RS33180' for NZ_RXUE01000001.1 Protein Homology CDS 0 104 -
dbxref : GenBank:WP_237758741.1
gbkey : CDS
id : cds-WP_237758741.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251876.1
locus_tag : DY959_RS33180
name : WP_237758741.1
parent : gene-DY959_RS33180
partial : true
product : hypothetical protein
protein_id : WP_237758741.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271750/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUE01000001.1 Protein Homology CDS 1 105 . - 0 ID=cds-WP_237758741.1;Parent=gene-DY959_RS33180;Dbxref=GenBank:WP_237758741.1;Name=WP_237758741.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251876.1;locus_tag=DY959_RS33180;partial=true;product=hypothetical protein;protein_id=WP_237758741.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY959_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY959_RS00005' for NZ_RXUE01000001.1 Protein Homology CDS 148 1308 -
dbxref : GenBank:WP_003119710.1
gbkey : CDS
go_function : ATP binding|0005524||IEA,ATP hydrolysis activity|0016887||IEA,ATPase-coupled transmembrane transporter activity|0042626||IEA,ABC-type transporter activity|0140359||IEA
id : cds-WP_003119710.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251877.1
locus_tag : DY959_RS00005
name : WP_003119710.1
ontology_term : GO:0005524,GO:0016887,GO:0042626,GO:0140359
parent : gene-DY959_RS00005
product : ABC transporter ATP-binding protein
protein_id : WP_003119710.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271750/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUE01000001.1 Protein Homology CDS 149 1309 . - 0 ID=cds-WP_003119710.1;Parent=gene-DY959_RS00005;Dbxref=GenBank:WP_003119710.1;Name=WP_003119710.1;Ontology_term=GO:0005524,GO:0016887,GO:0042626,GO:0140359;gbkey=CDS;go_function=ATP binding|0005524||IEA,ATP hydrolysis activity|0016887||IEA,ATPase-coupled transmembrane transporter activity|0042626||IEA,ABC-type transporter activity|0140359||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251877.1;locus_tag=DY959_RS00005;product=ABC transporter ATP-binding protein;protein_id=WP_003119710.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY959_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY959_RS00010' for NZ_RXUE01000001.1 Protein Homology CDS 1341 2186 -
dbxref : GenBank:WP_003091470.1
gbkey : CDS
go_process : carbohydrate transport|0008643||IEA,transmembrane transport|0055085||IEA
id : cds-WP_003091470.1
inference : COORDINATES: similar to AA sequen |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271751/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271751/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271751/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271751/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271751/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA06_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA06_RS00005' for NZ_RXWB01000001.1 Protein Homology CDS 18 626 -
dbxref : GenBank:WP_003161377.1
gbkey : CDS
gene : msrQ
id : cds-WP_003161377.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253379.1
locus_tag : DZA06_RS00005
name : WP_003161377.1
parent : gene-DZA06_RS00005
product : protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
protein_id : WP_003161377.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271751/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWB01000001.1 Protein Homology CDS 19 627 . - 0 ID=cds-WP_003161377.1;Parent=gene-DZA06_RS00005;Dbxref=GenBank:WP_003161377.1;Name=WP_003161377.1;gbkey=CDS;gene=msrQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253379.1;locus_tag=DZA06_RS00005;product=protein-methionine-sulfoxide reductase heme-binding subunit MsrQ;protein_id=WP_003161377.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA06_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA06_RS00010' for NZ_RXWB01000001.1 Protein Homology CDS 626 1639 -
dbxref : GenBank:WP_003116065.1
gbkey : CDS
gene : msrP
go_function : oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA
go_process : protein repair|0030091||IEA
id : cds-WP_003116065.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253380.1
locus_tag : DZA06_RS00010
name : WP_003116065.1
ontology_term : GO:0030091,GO:0016667,GO:0043546
parent : gene-DZA06_RS00010
product : protein-methionine-sulfoxide reductase catalytic subunit MsrP
protein_id : WP_003116065.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271751/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWB01000001.1 Protein Homology CDS 627 1640 . - 0 ID=cds-WP_003116065.1;Parent=gene-DZA06_RS00010;Dbxref=GenBank:WP_003116065.1;Name=WP_003116065.1;Ontology_term=GO:0030091,GO:0016667,GO:0043546;gbkey=CDS;gene=msrP;go_function=oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA;go_process=protein repair|0030091||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253380.1;locus_tag=DZA06_RS00010;product=protein-methionine-sulfoxide reductase catalytic subunit MsrP;protein_id=WP_003116065.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA06_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA06_RS00015' for NZ_RXWB01000001.1 Protein Homology CDS 1700 2515 -
dbxref : GenBank:WP_003095061.1
gbkey : CDS
gene : pssA
go_function : CDP-diacylglycerol-serine O-phosphat |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271752/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271752/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271752/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271752/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271752/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY996_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY996_RS00005' for NZ_RXVR01000001.1 Protein Homology CDS 0 753 -
dbxref : GenBank:WP_126584366.1
gbkey : CDS
id : cds-WP_126584366.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250565.1
locus_tag : DY996_RS00005
name : WP_126584366.1
parent : gene-DY996_RS00005
partial : true
product : Ig-like domain-containing protein
protein_id : WP_126584366.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271752/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVR01000001.1 Protein Homology CDS 1 754 . - 0 ID=cds-WP_126584366.1;Parent=gene-DY996_RS00005;Dbxref=GenBank:WP_126584366.1;Name=WP_126584366.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250565.1;locus_tag=DY996_RS00005;partial=true;product=Ig-like domain-containing protein;protein_id=WP_126584366.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY996_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY996_RS00010' for NZ_RXVR01000001.1 Protein Homology CDS 1253 2275 +
dbxref : GenBank:WP_003106674.1
gbkey : CDS
id : cds-WP_003106674.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250564.1
locus_tag : DY996_RS00010
name : WP_003106674.1
parent : gene-DY996_RS00010
product : transporter
protein_id : WP_003106674.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271752/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVR01000001.1 Protein Homology CDS 1254 2276 . + 0 ID=cds-WP_003106674.1;Parent=gene-DY996_RS00010;Dbxref=GenBank:WP_003106674.1;Name=WP_003106674.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250564.1;locus_tag=DY996_RS00010;product=transporter;protein_id=WP_003106674.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY996_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY996_RS00015' for NZ_RXVR01000001.1 Protein Homology CDS 2336 3127 +
dbxref : GenBank:WP_003106675.1
gbkey : CDS
id : cds-WP_003106675.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250563.1
locus_tag : DY996_RS00015
name : WP_003106675.1
parent : gene-DY996_RS00015
product : EcsC family protein
protein_id : WP_003106675.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271752/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVR01000001.1 Protein Homology CDS 2337 3128 . + 0 ID=cds-WP_003106675.1;Parent=gene-DY996_RS00015;Dbxref=GenBank:WP_003106675.1;Name=WP_003106675.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250563.1;locus_tag=DY996_RS00015;product |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271753/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271753/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271753/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271753/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271753/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY940_RS35220' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY940_RS35220' for NZ_RXTL01000001.1 GeneMarkS-2+ CDS 0 245 +
dbxref : GenBank:WP_221767941.1
gbkey : CDS
id : cds-WP_221767941.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY940_RS35220
name : WP_221767941.1
parent : gene-DY940_RS35220
partial : true
product : hypothetical protein
protein_id : WP_221767941.1
source : GeneMarkS-2+
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271753/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTL01000001.1 GeneMarkS-2+ CDS 1 246 . + 0 ID=cds-WP_221767941.1;Parent=gene-DY940_RS35220;Dbxref=GenBank:WP_221767941.1;Name=WP_221767941.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY940_RS35220;partial=true;product=hypothetical protein;protein_id=WP_221767941.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY940_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY940_RS00005' for NZ_RXTL01000001.1 Protein Homology CDS 194 1510 -
dbxref : GenBank:WP_003149666.1
gbkey : CDS
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003149666.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254057.1
locus_tag : DY940_RS00005
name : WP_003149666.1
ontology_term : GO:0055085,GO:0022857
parent : gene-DY940_RS00005
product : MFS transporter
protein_id : WP_003149666.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271753/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTL01000001.1 Protein Homology CDS 195 1511 . - 0 ID=cds-WP_003149666.1;Parent=gene-DY940_RS00005;Dbxref=GenBank:WP_003149666.1;Name=WP_003149666.1;Ontology_term=GO:0055085,GO:0022857;gbkey=CDS;go_function=transmembrane transporter activity|0022857||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254057.1;locus_tag=DY940_RS00005;product=MFS transporter;protein_id=WP_003149666.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY940_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY940_RS00010' for NZ_RXTL01000001.1 Protein Homology CDS 1798 2202 +
dbxref : GenBank:WP_003096677.1
gbkey : CDS
go_function : fatty acyl-CoA hydrolase activity|0047617||IEA
id : cds-WP_003096677.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254058.1
locus_tag : DY940_RS00010
name : WP_003096677.1
ontology_term : GO:0047617
parent : gene-DY940_RS00010
product : acyl-CoA thioesterase
protein_id : WP_003096677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scr |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271754/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271754/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271754/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271754/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271754/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY947_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY947_RS00005' for NZ_RXTS01000001.1 Protein Homology CDS 18 626 -
dbxref : GenBank:WP_016253925.1
gbkey : CDS
gene : msrQ
id : cds-WP_016253925.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253379.1
locus_tag : DY947_RS00005
name : WP_016253925.1
parent : gene-DY947_RS00005
product : protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
protein_id : WP_016253925.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271754/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTS01000001.1 Protein Homology CDS 19 627 . - 0 ID=cds-WP_016253925.1;Parent=gene-DY947_RS00005;Dbxref=GenBank:WP_016253925.1;Name=WP_016253925.1;gbkey=CDS;gene=msrQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253379.1;locus_tag=DY947_RS00005;product=protein-methionine-sulfoxide reductase heme-binding subunit MsrQ;protein_id=WP_016253925.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY947_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY947_RS00010' for NZ_RXTS01000001.1 Protein Homology CDS 626 1639 -
dbxref : GenBank:WP_003100146.1
gbkey : CDS
gene : msrP
go_function : oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA
go_process : protein repair|0030091||IEA
id : cds-WP_003100146.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253380.1
locus_tag : DY947_RS00010
name : WP_003100146.1
ontology_term : GO:0030091,GO:0016667,GO:0043546
parent : gene-DY947_RS00010
product : protein-methionine-sulfoxide reductase catalytic subunit MsrP
protein_id : WP_003100146.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271754/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTS01000001.1 Protein Homology CDS 627 1640 . - 0 ID=cds-WP_003100146.1;Parent=gene-DY947_RS00010;Dbxref=GenBank:WP_003100146.1;Name=WP_003100146.1;Ontology_term=GO:0030091,GO:0016667,GO:0043546;gbkey=CDS;gene=msrP;go_function=oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA;go_process=protein repair|0030091||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253380.1;locus_tag=DY947_RS00010;product=protein-methionine-sulfoxide reductase catalytic subunit MsrP;protein_id=WP_003100146.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY947_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY947_RS00015' for NZ_RXTS01000001.1 Protein Homology CDS 1700 2515 -
dbxref : GenBank:WP_003095061.1
gbkey : CDS
gene : pssA
go_function : CDP-diacylglycerol-serine O-phosphat |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271755/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271755/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271755/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271755/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271755/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY976_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY976_RS00005' for NZ_RXUV01000001.1 Protein Homology CDS 294 3389 -
dbxref : GenBank:WP_126432350.1
gbkey : CDS
gene : dnaE2
id : cds-WP_126432350.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY976_RS00005
name : WP_126432350.1
parent : gene-DY976_RS00005
product : error-prone DNA polymerase
protein_id : WP_126432350.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271755/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUV01000001.1 Protein Homology CDS 295 3390 . - 0 ID=cds-WP_126432350.1;Parent=gene-DY976_RS00005;Dbxref=GenBank:WP_126432350.1;Name=WP_126432350.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY976_RS00005;product=error-prone DNA polymerase;protein_id=WP_126432350.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY976_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY976_RS00010' for NZ_RXUV01000001.1 Protein Homology CDS 3365 4780 -
dbxref : GenBank:WP_003116540.1
gbkey : CDS
id : cds-WP_003116540.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY976_RS00010
name : WP_003116540.1
parent : gene-DY976_RS00010
product : Y-family DNA polymerase
protein_id : WP_003116540.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271755/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUV01000001.1 Protein Homology CDS 3366 4781 . - 0 ID=cds-WP_003116540.1;Parent=gene-DY976_RS00010;Dbxref=GenBank:WP_003116540.1;Name=WP_003116540.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY976_RS00010;product=Y-family DNA polymerase;protein_id=WP_003116540.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY976_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY976_RS00015' for NZ_RXUV01000001.1 Protein Homology CDS 4788 5393 -
dbxref : GenBank:WP_031627677.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031627677.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003296675.1
locus_tag : DY976_RS00015
name : WP_031627677.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY976_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031627677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271755/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUV01000001.1 Protein Homology CDS 4789 5394 . - 0 ID=cds-WP_031627677.1;Parent=gene-DY976_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271756/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271756/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271756/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271756/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271756/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY928_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY928_RS00010' for NZ_RXSZ01000001.1 Protein Homology CDS 452 1204 +
dbxref : GenBank:WP_121335255.1
gbkey : CDS
id : cds-WP_121335255.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248988.1
locus_tag : DY928_RS00010
name : WP_121335255.1
parent : gene-DY928_RS00010
product : gamma-glutamyl-gamma-aminobutyrate hydrolase family protein
protein_id : WP_121335255.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271756/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXSZ01000001.1 Protein Homology CDS 453 1205 . + 0 ID=cds-WP_121335255.1;Parent=gene-DY928_RS00010;Dbxref=GenBank:WP_121335255.1;Name=WP_121335255.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248988.1;locus_tag=DY928_RS00010;product=gamma-glutamyl-gamma-aminobutyrate hydrolase family protein;protein_id=WP_121335255.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY928_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY928_RS00015' for NZ_RXSZ01000001.1 Protein Homology CDS 1245 2603 +
dbxref : GenBank:WP_003084290.1
gbkey : CDS
go_function : glutamine synthetase activity|0004356||IEA,ATP binding|0005524||IEA
go_process : glutamine biosynthetic process|0006542||IEA
id : cds-WP_003084290.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248989.1
locus_tag : DY928_RS00015
name : WP_003084290.1
ontology_term : GO:0006542,GO:0004356,GO:0005524
parent : gene-DY928_RS00015
product : glutamine synthetase family protein
protein_id : WP_003084290.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271756/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXSZ01000001.1 Protein Homology CDS 1246 2604 . + 0 ID=cds-WP_003084290.1;Parent=gene-DY928_RS00015;Dbxref=GenBank:WP_003084290.1;Name=WP_003084290.1;Ontology_term=GO:0006542,GO:0004356,GO:0005524;gbkey=CDS;go_function=glutamine synthetase activity|0004356||IEA,ATP binding|0005524||IEA;go_process=glutamine biosynthetic process|0006542||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248989.1;locus_tag=DY928_RS00015;product=glutamine synthetase family protein;protein_id=WP_003084290.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY928_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY928_RS00020' for NZ_RXSZ01000001.1 Protein Homology CDS 2669 4039 +
dbxref : GenBank:WP_003084297.1
gbkey : CDS
gene : spuC
id : cds-WP_003084297.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248990.1
locus_tag : DY928_RS00020
name : WP_003084297.1
parent : gene-DY928_RS00020
product : putrescine--pyruvate aminotransferase
protein |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271757/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271757/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271757/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271757/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271757/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY935_RS33605' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY935_RS33605' for NZ_RXTG01000001.1 Protein Homology CDS 0 180 -
dbxref : GenBank:WP_148107089.1
gbkey : CDS
go_component : cytoplasm|0005737||IEA
go_function : nucleotide binding|0000166||IEA,magnesium ion binding|0000287||IEA,5'-nucleotidase activity|0008253||IEA
go_process : nucleotide metabolic process|0009117||IEA
id : cds-WP_148107089.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_008375204.1
locus_tag : DY935_RS33605
name : WP_148107089.1
ontology_term : GO:0009117,GO:0000166,GO:0000287,GO:0008253,GO:0005737
parent : gene-DY935_RS33605
partial : true
product : 5'-nucleotidase
protein_id : WP_148107089.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271757/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTG01000001.1 Protein Homology CDS 1 181 . - 0 ID=cds-WP_148107089.1;Parent=gene-DY935_RS33605;Dbxref=GenBank:WP_148107089.1;Name=WP_148107089.1;Ontology_term=GO:0009117,GO:0000166,GO:0000287,GO:0008253,GO:0005737;gbkey=CDS;go_component=cytoplasm|0005737||IEA;go_function=nucleotide binding|0000166||IEA,magnesium ion binding|0000287||IEA,5'-nucleotidase activity|0008253||IEA;go_process=nucleotide metabolic process|0009117||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008375204.1;locus_tag=DY935_RS33605;partial=true;product=5'-nucleotidase;protein_id=WP_148107089.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY935_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY935_RS00010' for NZ_RXTG01000001.1 Protein Homology CDS 293 1540 -
dbxref : GenBank:WP_003086547.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA
go_process : deoxyribonucleotide biosynthetic process|0009263||IEA
id : cds-WP_003086547.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249846.1
locus_tag : DY935_RS00010
name : WP_003086547.1
ontology_term : GO:0009263,GO:0016491
parent : gene-DY935_RS00010
product : ribonucleotide-diphosphate reductase subunit beta
protein_id : WP_003086547.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271757/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTG01000001.1 Protein Homology CDS 294 1541 . - 0 ID=cds-WP_003086547.1;Parent=gene-DY935_RS00010;Dbxref=GenBank:WP_003086547.1;Name=WP_003086547.1;Ontology_term=GO:0009263,GO:0016491;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA;go_process=deoxyribonucleotide biosynthetic process|0009263||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249846.1;locus_tag=DY935_RS00010;product=ribonucleotide-diphosphate reductase subunit beta;protein_id=WP_003086547.1;transl_table=11'
WARNING_TRANSCRIPT_ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271758/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271758/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271758/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271758/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271758/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY932_RS35195' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY932_RS35195' for NZ_RXTD01000001.1 GeneMarkS-2+ CDS 0 245 +
dbxref : GenBank:WP_221767941.1
gbkey : CDS
id : cds-WP_221767941.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY932_RS35195
name : WP_221767941.1
parent : gene-DY932_RS35195
partial : true
product : hypothetical protein
protein_id : WP_221767941.1
source : GeneMarkS-2+
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271758/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTD01000001.1 GeneMarkS-2+ CDS 1 246 . + 0 ID=cds-WP_221767941.1;Parent=gene-DY932_RS35195;Dbxref=GenBank:WP_221767941.1;Name=WP_221767941.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY932_RS35195;partial=true;product=hypothetical protein;protein_id=WP_221767941.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY932_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY932_RS00005' for NZ_RXTD01000001.1 Protein Homology CDS 194 1510 -
dbxref : GenBank:WP_003149666.1
gbkey : CDS
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003149666.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254057.1
locus_tag : DY932_RS00005
name : WP_003149666.1
ontology_term : GO:0055085,GO:0022857
parent : gene-DY932_RS00005
product : MFS transporter
protein_id : WP_003149666.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271758/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTD01000001.1 Protein Homology CDS 195 1511 . - 0 ID=cds-WP_003149666.1;Parent=gene-DY932_RS00005;Dbxref=GenBank:WP_003149666.1;Name=WP_003149666.1;Ontology_term=GO:0055085,GO:0022857;gbkey=CDS;go_function=transmembrane transporter activity|0022857||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254057.1;locus_tag=DY932_RS00005;product=MFS transporter;protein_id=WP_003149666.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY932_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY932_RS00010' for NZ_RXTD01000001.1 Protein Homology CDS 1798 2202 +
dbxref : GenBank:WP_003096677.1
gbkey : CDS
go_function : hydrolase activity|0016787||IEA,thiolester hydrolase activity|0016790||IEA
id : cds-WP_003096677.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254058.1
locus_tag : DY932_RS00010
name : WP_003096677.1
ontology_term : GO:0016787,GO:0016790
parent : gene-DY932_RS00010
product : acyl-CoA thioesterase
protein_id : WP_003096677.1
source : Protein Homology
transl_table : 11
|
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271759/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271759/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271759/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271759/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271759/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY968_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY968_RS00005' for NZ_RXUN01000001.1 Protein Homology CDS 85 1107 +
dbxref : GenBank:WP_112234279.1
gbkey : CDS
id : cds-WP_112234279.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_017939357.1
locus_tag : DY968_RS00005
name : WP_112234279.1
parent : gene-DY968_RS00005
product : LPS O-antigen chain length determinant protein WzzB
protein_id : WP_112234279.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271759/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUN01000001.1 Protein Homology CDS 86 1108 . + 0 ID=cds-WP_112234279.1;Parent=gene-DY968_RS00005;Dbxref=GenBank:WP_112234279.1;Name=WP_112234279.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_017939357.1;locus_tag=DY968_RS00005;product=LPS O-antigen chain length determinant protein WzzB;protein_id=WP_112234279.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY968_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY968_RS00010' for NZ_RXUN01000001.1 Protein Homology CDS 1194 2459 +
dbxref : GenBank:WP_057386782.1
gbkey : CDS
gene : tviB
go_function : oxidoreductase activity|0016491||IEA,NAD binding|0051287||IEA
go_process : polysaccharide biosynthetic process|0000271||IEA
id : cds-WP_057386782.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012613866.1
locus_tag : DY968_RS00010
name : WP_057386782.1
ontology_term : GO:0000271,GO:0016491,GO:0051287
parent : gene-DY968_RS00010
product : Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB
protein_id : WP_057386782.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271759/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUN01000001.1 Protein Homology CDS 1195 2460 . + 0 ID=cds-WP_057386782.1;Parent=gene-DY968_RS00010;Dbxref=GenBank:WP_057386782.1;Name=WP_057386782.1;Ontology_term=GO:0000271,GO:0016491,GO:0051287;gbkey=CDS;gene=tviB;go_function=oxidoreductase activity|0016491||IEA,NAD binding|0051287||IEA;go_process=polysaccharide biosynthetic process|0000271||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012613866.1;locus_tag=DY968_RS00010;product=Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB;protein_id=WP_057386782.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY968_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY968_RS00015' for NZ_RXUN01000001.1 Protein Homology CDS 2469 3494 +
dbxref : GenBank:WP_079743188.1
gbkey : CDS
go_function : catalytic activity|0003824||IEA
id : cds-WP_079743188.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_00316331 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271760/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271760/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271760/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271760/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271760/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY936_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY936_RS00005' for NZ_RXTH01000001.1 Protein Homology CDS 0 931 +
dbxref : GenBank:WP_176425776.1
gbkey : CDS
go_function : glycosyltransferase activity|0016757||IEA
id : cds-WP_176425776.1
inference : COORDINATES: protein motif:HMM:NF025072.5
locus_tag : DY936_RS00005
name : WP_176425776.1
ontology_term : GO:0016757
parent : gene-DY936_RS00005
partial : true
product : glycosyltransferase family 4 protein
protein_id : WP_176425776.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271760/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTH01000001.1 Protein Homology CDS 1 932 . + 2 ID=cds-WP_176425776.1;Parent=gene-DY936_RS00005;Dbxref=GenBank:WP_176425776.1;Name=WP_176425776.1;Ontology_term=GO:0016757;gbkey=CDS;go_function=glycosyltransferase activity|0016757||IEA;inference=COORDINATES: protein motif:HMM:NF025072.5;locus_tag=DY936_RS00005;partial=true;product=glycosyltransferase family 4 protein;protein_id=WP_176425776.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY936_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY936_RS00010' for NZ_RXTH01000001.1 Protein Homology CDS 936 2819 +
dbxref : GenBank:WP_003122252.1
gbkey : CDS
gene : asnB
go_function : asparagine synthase (glutamine-hydrolyzing) activity|0004066||IEA
go_process : asparagine biosynthetic process|0006529||IEA
id : cds-WP_003122252.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012613869.1
locus_tag : DY936_RS00010
name : WP_003122252.1
ontology_term : GO:0006529,GO:0004066
parent : gene-DY936_RS00010
product : asparagine synthase (glutamine-hydrolyzing)
protein_id : WP_003122252.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271760/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTH01000001.1 Protein Homology CDS 937 2820 . + 0 ID=cds-WP_003122252.1;Parent=gene-DY936_RS00010;Dbxref=GenBank:WP_003122252.1;Name=WP_003122252.1;Ontology_term=GO:0006529,GO:0004066;gbkey=CDS;gene=asnB;go_function=asparagine synthase (glutamine-hydrolyzing) activity|0004066||IEA;go_process=asparagine biosynthetic process|0006529||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012613869.1;locus_tag=DY936_RS00010;product=asparagine synthase (glutamine-hydrolyzing);protein_id=WP_003122252.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY936_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY936_RS00015' for NZ_RXTH01000001.1 Protein Homology CDS 2816 3967 +
dbxref : GenBank:WP_003122253.1
gbkey : CDS
id : cds-WP_003122253.1
inference : COORDINATES: similar to AA sequence:RefS |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271761/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271761/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271761/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271761/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271761/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY938_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY938_RS00005' for NZ_RXTJ01000001.1 Protein Homology CDS 0 265 -
dbxref : GenBank:WP_043103703.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA
id : cds-WP_043103703.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252711.1
locus_tag : DY938_RS00005
name : WP_043103703.1
ontology_term : GO:0016491
parent : gene-DY938_RS00005
partial : true
product : aldehyde dehydrogenase family protein
protein_id : WP_043103703.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271761/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTJ01000001.1 Protein Homology CDS 1 266 . - 0 ID=cds-WP_043103703.1;Parent=gene-DY938_RS00005;Dbxref=GenBank:WP_043103703.1;Name=WP_043103703.1;Ontology_term=GO:0016491;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252711.1;locus_tag=DY938_RS00005;partial=true;product=aldehyde dehydrogenase family protein;protein_id=WP_043103703.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY938_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY938_RS00010' for NZ_RXTJ01000001.1 Protein Homology CDS 604 2535 +
dbxref : GenBank:WP_126428126.1
gbkey : CDS
gene : eatR
id : cds-WP_126428126.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252710.1
locus_tag : DY938_RS00010
name : WP_126428126.1
parent : gene-DY938_RS00010
product : sigma-54-dependent transcriptional regulator EatR
protein_id : WP_126428126.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271761/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTJ01000001.1 Protein Homology CDS 605 2536 . + 0 ID=cds-WP_126428126.1;Parent=gene-DY938_RS00010;Dbxref=GenBank:WP_126428126.1;Name=WP_126428126.1;gbkey=CDS;gene=eatR;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252710.1;locus_tag=DY938_RS00010;product=sigma-54-dependent transcriptional regulator EatR;protein_id=WP_126428126.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY938_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY938_RS00015' for NZ_RXTJ01000001.1 Protein Homology CDS 2693 4048 +
dbxref : GenBank:WP_003124067.1
gbkey : CDS
gene : mpl
go_function : acid-amino acid ligase activity|0016881||IEA
go_process : peptidoglycan biosynthetic process|0009252||IEA,cell wall organization|0071555||IEA
id : cds-WP_003124067.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252709.1
locus_tag : DY938_RS00015
name : WP_003124067.1
ontology_term : GO:0009252,GO:0071555,GO:0016881
parent : gene-DY938_RS00015
|
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271762/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271762/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271762/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271762/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271762/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-C9899_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-C9899_RS00005' for NZ_RXSX01000001.1 Protein Homology CDS 35 523 -
dbxref : GenBank:WP_003123955.1
gbkey : CDS
gene : phzB
id : cds-WP_003123955.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252900.1
locus_tag : C9899_RS00005
name : WP_003123955.1
parent : gene-C9899_RS00005
product : phenazine biosynthesis protein PhzB
protein_id : WP_003123955.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271762/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXSX01000001.1 Protein Homology CDS 36 524 . - 0 ID=cds-WP_003123955.1;Parent=gene-C9899_RS00005;Dbxref=GenBank:WP_003123955.1;Name=WP_003123955.1;gbkey=CDS;gene=phzB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252900.1;locus_tag=C9899_RS00005;product=phenazine biosynthesis protein PhzB;protein_id=WP_003123955.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-C9899_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-C9899_RS00010' for NZ_RXSX01000001.1 Protein Homology CDS 553 1041 -
dbxref : GenBank:WP_003114729.1
gbkey : CDS
gene : phzA
id : cds-WP_003114729.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252899.1
locus_tag : C9899_RS00010
name : WP_003114729.1
parent : gene-C9899_RS00010
product : phenazine biosynthesis protein PhzA
protein_id : WP_003114729.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271762/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXSX01000001.1 Protein Homology CDS 554 1042 . - 0 ID=cds-WP_003114729.1;Parent=gene-C9899_RS00010;Dbxref=GenBank:WP_003114729.1;Name=WP_003114729.1;gbkey=CDS;gene=phzA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252899.1;locus_tag=C9899_RS00010;product=phenazine biosynthesis protein PhzA;protein_id=WP_003114729.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-C9899_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-C9899_RS00020' for NZ_RXSX01000001.1 Protein Homology CDS 1738 2742 +
dbxref : GenBank:WP_003093617.1
gbkey : CDS
gene : phzM
id : cds-WP_003093617.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252898.1
locus_tag : C9899_RS00020
name : WP_003093617.1
parent : gene-C9899_RS00020
product : phenazine-1-carboxylate N-methyltransferase PhzM
protein_id : WP_003093617.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271762/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXSX01000001.1 Protein Homology CDS 1739 2743 . + 0 ID=cds-WP_003093617.1;Parent=gene-C9899_RS00020;Dbxref=GenBank:WP_003093617.1;Name=WP_003093617.1;gbkey=CDS;gene=phzM;infe |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271763/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271763/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271763/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271763/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271763/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ64_RS15975' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ64_RS15975' for NZ_RHSB01000010.1 GeneMarkS-2+ CDS 709 1641 +
dbxref : GenBank:WP_003084116.1
gbkey : CDS
id : cds-WP_003084116.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : EGJ64_RS15975
name : WP_003084116.1
parent : gene-EGJ64_RS15975
product : hypothetical protein
protein_id : WP_003084116.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271763/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSB01000010.1 GeneMarkS-2+ CDS 710 1642 . + 0 ID=cds-WP_003084116.1;Parent=gene-EGJ64_RS15975;Dbxref=GenBank:WP_003084116.1;Name=WP_003084116.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=EGJ64_RS15975;product=hypothetical protein;protein_id=WP_003084116.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ64_RS15980' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ64_RS15980' for NZ_RHSB01000010.1 Protein Homology CDS 1805 2491 +
dbxref : GenBank:WP_003106170.1
gbkey : CDS
go_component : plasma membrane|0005886||IEA,membrane|0016020||IEA
id : cds-WP_003106170.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248946.1
locus_tag : EGJ64_RS15980
name : WP_003106170.1
ontology_term : GO:0005886,GO:0016020
parent : gene-EGJ64_RS15980
product : YoaK family protein
protein_id : WP_003106170.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271763/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSB01000010.1 Protein Homology CDS 1806 2492 . + 0 ID=cds-WP_003106170.1;Parent=gene-EGJ64_RS15980;Dbxref=GenBank:WP_003106170.1;Name=WP_003106170.1;Ontology_term=GO:0005886,GO:0016020;gbkey=CDS;go_component=plasma membrane|0005886||IEA,membrane|0016020||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248946.1;locus_tag=EGJ64_RS15980;product=YoaK family protein;protein_id=WP_003106170.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ64_RS15985' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ64_RS15985' for NZ_RHSB01000010.1 Protein Homology CDS 2612 4102 +
dbxref : GenBank:WP_003084112.1
gbkey : CDS
gene : hudA
id : cds-WP_003084112.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248945.1
locus_tag : EGJ64_RS15985
name : WP_003084112.1
parent : gene-EGJ64_RS15985
product : UbiD family decarboxylase HudA
protein_id : WP_003084112.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271763/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSB01000010.1 Protein Homology CDS 2613 4103 . + 0 ID=cds-WP_003084112.1;Parent=gene-EGJ64_RS15985;Dbxref=GenBank:WP_003084 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271764/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271764/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271764/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271764/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271764/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ69_RS14350' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ69_RS14350' for NZ_RHRZ01000010.1 Protein Homology CDS 185 1021 +
dbxref : GenBank:WP_003086930.1
gbkey : CDS
go_component : cytoplasm|0005737||IEA
go_function : isomerase activity|0016853||IEA
go_process : biosynthetic process|0009058||IEA
id : cds-WP_003086930.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250058.1
locus_tag : EGJ69_RS14350
name : WP_003086930.1
ontology_term : GO:0009058,GO:0016853,GO:0005737
parent : gene-EGJ69_RS14350
product : PhzF family phenazine biosynthesis protein
protein_id : WP_003086930.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271764/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHRZ01000010.1 Protein Homology CDS 186 1022 . + 0 ID=cds-WP_003086930.1;Parent=gene-EGJ69_RS14350;Dbxref=GenBank:WP_003086930.1;Name=WP_003086930.1;Ontology_term=GO:0009058,GO:0016853,GO:0005737;gbkey=CDS;go_component=cytoplasm|0005737||IEA;go_function=isomerase activity|0016853||IEA;go_process=biosynthetic process|0009058||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250058.1;locus_tag=EGJ69_RS14350;product=PhzF family phenazine biosynthesis protein;protein_id=WP_003086930.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ69_RS14355' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ69_RS14355' for NZ_RHRZ01000010.1 Protein Homology CDS 1181 3622 -
dbxref : GenBank:WP_003086926.1
gbkey : CDS
go_component : cell outer membrane|0009279||IEA
go_function : siderophore-iron transmembrane transporter activity|0015343||IEA,signaling receptor activity|0038023||IEA
go_process : siderophore transport|0015891||IEA
id : cds-WP_003086926.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250056.1
locus_tag : EGJ69_RS14355
name : WP_003086926.1
ontology_term : GO:0015891,GO:0015343,GO:0038023,GO:0009279
parent : gene-EGJ69_RS14355
product : TonB-dependent siderophore receptor
protein_id : WP_003086926.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271764/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHRZ01000010.1 Protein Homology CDS 1182 3623 . - 0 ID=cds-WP_003086926.1;Parent=gene-EGJ69_RS14355;Dbxref=GenBank:WP_003086926.1;Name=WP_003086926.1;Ontology_term=GO:0015891,GO:0015343,GO:0038023,GO:0009279;gbkey=CDS;go_component=cell outer membrane|0009279||IEA;go_function=siderophore-iron transmembrane transporter activity|0015343||IEA,signaling receptor activity|0038023||IEA;go_process=siderophore transport|0015891||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250056.1;locus_tag=EGJ69_RS14355;product=TonB-dependent siderophore receptor;protein_id=WP_003086926.1;transl_table=11'
WARNING_TRANSCRI |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271765/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271765/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271765/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271765/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271765/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ78_RS32865' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ78_RS32865' for NZ_RHTA01000100.1 Protein Homology CDS 0 119 -
dbxref : GenBank:WP_241486202.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
id : cds-WP_241486202.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_000679427.1
locus_tag : EGJ78_RS32865
name : WP_241486202.1
ontology_term : GO:0022857,GO:0016020
parent : gene-EGJ78_RS32865
partial : true
product : SMR family transporter
protein_id : WP_241486202.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271765/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHTA01000100.1 Protein Homology CDS 1 120 . - 0 ID=cds-WP_241486202.1;Parent=gene-EGJ78_RS32865;Dbxref=GenBank:WP_241486202.1;Name=WP_241486202.1;Ontology_term=GO:0022857,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=transmembrane transporter activity|0022857||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_000679427.1;locus_tag=EGJ78_RS32865;partial=true;product=SMR family transporter;protein_id=WP_241486202.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ78_RS32870' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ78_RS32870' for NZ_RHTA01000100.1 Protein Homology CDS 236 514 -
dbxref : GenBank:WP_108092422.1
gbkey : CDS
id : cds-WP_108092422.1
inference : COORDINATES: protein motif:HMM:NF017990.5
locus_tag : EGJ78_RS32870
name : WP_108092422.1
parent : gene-EGJ78_RS32870
product : DUF1010 domain-containing protein
protein_id : WP_108092422.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271765/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHTA01000100.1 Protein Homology CDS 237 515 . - 0 ID=cds-WP_108092422.1;Parent=gene-EGJ78_RS32870;Dbxref=GenBank:WP_108092422.1;Name=WP_108092422.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF017990.5;locus_tag=EGJ78_RS32870;product=DUF1010 domain-containing protein;protein_id=WP_108092422.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ78_RS32875' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ78_RS32875' for NZ_RHTA01000100.1 Protein Homology CDS 556 1401 -
dbxref : GenBank:WP_022675713.1
gbkey : CDS
id : cds-WP_022675713.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_048608579.1
locus_tag : EGJ78_RS32875
name : WP_022675713.1
parent : gene-EGJ78_RS32875
product : ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA6
protein_id : WP_022675713.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271765/work |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271766/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271766/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271766/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271766/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271766/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ96_RS34245' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ96_RS34245' for NZ_RHSY01000100.1 Protein Homology CDS 100 468 -
dbxref : GenBank:WP_003127781.1
gbkey : CDS
id : cds-WP_003127781.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_019485949.1
locus_tag : EGJ96_RS34245
name : WP_003127781.1
parent : gene-EGJ96_RS34245
product : Mor transcription activator family protein
protein_id : WP_003127781.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271766/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSY01000100.1 Protein Homology CDS 101 469 . - 0 ID=cds-WP_003127781.1;Parent=gene-EGJ96_RS34245;Dbxref=GenBank:WP_003127781.1;Name=WP_003127781.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_019485949.1;locus_tag=EGJ96_RS34245;product=Mor transcription activator family protein;protein_id=WP_003127781.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ96_RS34250' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ96_RS34250' for NZ_RHSY01000100.1 Protein Homology CDS 465 1013 -
dbxref : GenBank:WP_003117363.1
gbkey : CDS
id : cds-WP_003117363.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003117363.1
locus_tag : EGJ96_RS34250
name : WP_003117363.1
parent : gene-EGJ96_RS34250
product : hypothetical protein
protein_id : WP_003117363.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271766/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSY01000100.1 Protein Homology CDS 466 1014 . - 0 ID=cds-WP_003117363.1;Parent=gene-EGJ96_RS34250;Dbxref=GenBank:WP_003117363.1;Name=WP_003117363.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003117363.1;locus_tag=EGJ96_RS34250;product=hypothetical protein;protein_id=WP_003117363.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ96_RS34255' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ96_RS34255' for NZ_RHSY01000100.1 Protein Homology CDS 1013 1561 -
dbxref : GenBank:WP_228775689.1
end_range : 1562,.
gbkey : CDS
id : cds-WP_228775689.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003117362.1
locus_tag : EGJ96_RS34255
name : WP_228775689.1
parent : gene-EGJ96_RS34255
partial : true
product : gp16 family protein
protein_id : WP_228775689.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271766/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSY01000100.1 Protein Homology CDS 1014 1562 . - 0 ID=cds-WP_228775689.1;Parent=gene-EGJ96_RS34255;Dbxref=GenBank:WP_228775689.1;Name=WP_228775689.1;end_range=1562,.;gbkey=CDS;inference=COORDINATES: similar to AA sequence:Re |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271767/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271767/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271767/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271767/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271767/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ92_RS32190' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ92_RS32190' for NZ_RHTB01000100.1 Protein Homology CDS 0 649 +
dbxref : GenBank:WP_260467232.1
gbkey : CDS
id : cds-WP_260467232.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252004.1
locus_tag : EGJ92_RS32190
name : WP_260467232.1
parent : gene-EGJ92_RS32190
partial : true
product : phosphonate ABC transporter ATP-binding protein
protein_id : WP_260467232.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271767/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHTB01000100.1 Protein Homology CDS 1 650 . + 2 ID=cds-WP_260467232.1;Parent=gene-EGJ92_RS32190;Dbxref=GenBank:WP_260467232.1;Name=WP_260467232.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252004.1;locus_tag=EGJ92_RS32190;partial=true;product=phosphonate ABC transporter ATP-binding protein;protein_id=WP_260467232.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ92_RS32195' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ92_RS32195' for NZ_RHTB01000100.1 Protein Homology CDS 643 1476 +
dbxref : GenBank:WP_003091683.1
gbkey : CDS
id : cds-WP_003091683.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252005.1
locus_tag : EGJ92_RS32195
name : WP_003091683.1
parent : gene-EGJ92_RS32195
product : PhnE/PtxC family ABC transporter permease
protein_id : WP_003091683.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271767/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHTB01000100.1 Protein Homology CDS 644 1477 . + 0 ID=cds-WP_003091683.1;Parent=gene-EGJ92_RS32195;Dbxref=GenBank:WP_003091683.1;Name=WP_003091683.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252005.1;locus_tag=EGJ92_RS32195;product=PhnE/PtxC family ABC transporter permease;protein_id=WP_003091683.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ92_RS32200' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ92_RS32200' for NZ_RHTB01000100.1 Protein Homology CDS 1473 2243 +
dbxref : GenBank:WP_125910229.1
gbkey : CDS
gene : phnE
go_component : plasma membrane|0005886||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ABC-type phosphonate transporter activity|0015416||IEA
go_process : organic phosphonate transport|0015716||IEA
id : cds-WP_125910229.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252006.1
locus_tag : EGJ92_RS32200
name : WP_125910229.1
ontology_term : GO:0015716,GO:0015416,GO:0005886,GO:0055052
parent : gene-EGJ92_RS32200
product : phosphonate ABC transporter%2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271768/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271768/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271768/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_RHSI01000100.1:1-991) does not include 'gene-EGJ75_RS33405' (NZ_RHSI01000101.1:1-991). Created new gene 'null.2' (NZ_RHSI01000101.1:1-991). File '/jetstream2/scratch/main/jobs/72271768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSI01000101.1 RefSeq pseudogene 1 991 . + . ID=gene-EGJ75_RS33405;Name=EGJ75_RS33405;end_range=991,.;gbkey=Gene;gene_biotype=pseudogene;locus_tag=EGJ75_RS33405;old_locus_tag=EGJ75_33245;partial=true;pseudo=true;start_range=.,1'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_RHSI01000100.1:1-991) does not include 'gene-EGJ75_RS33410' (NZ_RHSI01000102.1:1-226). Created new gene 'null.3' (NZ_RHSI01000102.1:1-226). File '/jetstream2/scratch/main/jobs/72271768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 21 'NZ_RHSI01000102.1 RefSeq pseudogene 1 226 . + . ID=gene-EGJ75_RS33410;Name=EGJ75_RS33410;gbkey=Gene;gene_biotype=pseudogene;locus_tag=EGJ75_RS33410;old_locus_tag=EGJ75_33250;partial=true;pseudo=true;start_range=.,1'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_RHSI01000100.1:1-991) does not include 'gene-EGJ75_RS33415' (NZ_RHSI01000102.1:241-971). Created new gene 'null.4' (NZ_RHSI01000102.1:241-971). File '/jetstream2/scratch/main/jobs/72271768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 23 'NZ_RHSI01000102.1 RefSeq pseudogene 241 971 . + . ID=gene-EGJ75_RS33415;Name=EGJ75_RS33415;end_range=971,.;gbkey=Gene;gene_biotype=pseudogene;locus_tag=EGJ75_RS33415;old_locus_tag=EGJ75_33255;partial=true;pseudo=true'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ75_RS33425' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ75_RS33425' for NZ_RHSI01000104.1 Protein Homology CDS 0 937 +
dbxref : GenBank:WP_185761647.1
end_range : 938,.
gbkey : CDS
id : cds-WP_185761647.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003086160.1
locus_tag : EGJ75_RS33425
name : WP_185761647.1
parent : gene-EGJ75_RS33425
partial : true
product : TraC family protein
protein_id : WP_185761647.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271768/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 34 'NZ_RHSI01000104.1 Protein Homology CDS 1 938 . + 0 ID=cds-WP_185761647.1;Parent=gene-EGJ75_RS33425;Dbxref=GenBank:WP_185761647.1;Name=WP_185761647.1;end_range=938,.;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003086160.1;locus_tag=EGJ75_RS33425;partial=true;product=TraC family protein;protein_id=WP_185761647.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ75_RS33430' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ75_RS33430' for NZ_RHSI01000105.1 Protein Homology CDS 0 920 -
dbxref : GenBank:WP_124988511.1
end_range : 921,.
gbkey : CDS
gene : tssI
go_process : protein secretion by the type VI secretion system|00 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271769/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271769/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271769/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271769/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271769/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ84_RS34145' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ84_RS34145' for NZ_RHSF01000100.1 Protein Homology CDS 0 1076 +
dbxref : GenBank:WP_031691545.1
end_range : 1077,.
gbkey : CDS
gene : oprB
id : cds-WP_031691545.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251876.1
locus_tag : EGJ84_RS34145
name : WP_031691545.1
parent : gene-EGJ84_RS34145
partial : true
product : carbohydrate porin OprB
protein_id : WP_031691545.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271769/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSF01000100.1 Protein Homology CDS 1 1077 . + 2 ID=cds-WP_031691545.1;Parent=gene-EGJ84_RS34145;Dbxref=GenBank:WP_031691545.1;Name=WP_031691545.1;end_range=1077,.;gbkey=CDS;gene=oprB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251876.1;locus_tag=EGJ84_RS34145;partial=true;product=carbohydrate porin OprB;protein_id=WP_031691545.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ84_RS34155' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ84_RS34155' for NZ_RHSF01000102.1 GeneMarkS-2+ CDS 185 805 -
dbxref : GenBank:WP_031632581.1
gbkey : CDS
id : cds-WP_031632581.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : EGJ84_RS34155
name : WP_031632581.1
parent : gene-EGJ84_RS34155
product : hypothetical protein
protein_id : WP_031632581.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271769/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 22 'NZ_RHSF01000102.1 GeneMarkS-2+ CDS 186 806 . - 0 ID=cds-WP_031632581.1;Parent=gene-EGJ84_RS34155;Dbxref=GenBank:WP_031632581.1;Name=WP_031632581.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=EGJ84_RS34155;product=hypothetical protein;protein_id=WP_031632581.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ84_RS34160' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ84_RS34160' for NZ_RHSF01000103.1 Protein Homology CDS 0 1006 -
dbxref : GenBank:WP_125939925.1
end_range : 1007,.
gbkey : CDS
id : cds-WP_125939925.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251152.1
locus_tag : EGJ84_RS34160
name : WP_125939925.1
parent : gene-EGJ84_RS34160
partial : true
product : filamentous hemagglutinin N-terminal domain-containing protein
protein_id : WP_125939925.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271769/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 27 'NZ_RHSF01000103.1 Protein Homology CDS 1 1007 . - 0 ID=cds-WP_125939925.1;Parent=gene-EGJ84_RS34160;Dbxref=GenBank:WP_125939925.1;N |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271770/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271770/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271770/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271770/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271770/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGK62_RS34205' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGK62_RS34205' for NZ_RHSZ01000100.1 Protein Homology CDS 0 181 -
dbxref : GenBank:WP_054080540.1
gbkey : CDS
id : cds-WP_054080540.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_076611480.1
locus_tag : EGK62_RS34205
name : WP_054080540.1
parent : gene-EGK62_RS34205
partial : true
product : transposase
protein_id : WP_054080540.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271770/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSZ01000100.1 Protein Homology CDS 1 182 . - 0 ID=cds-WP_054080540.1;Parent=gene-EGK62_RS34205;Dbxref=GenBank:WP_054080540.1;Name=WP_054080540.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_076611480.1;locus_tag=EGK62_RS34205;partial=true;product=transposase;protein_id=WP_054080540.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGK62_RS35690' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGK62_RS35690' for NZ_RHSZ01000100.1 Protein Homology CDS 859 2052 +
dbxref : GenBank:WP_003112561.1
gbkey : CDS
gene : pyoS5
id : cds-WP_003112561.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_153570677.1
locus_tag : EGK62_RS35690
name : WP_003112561.1
parent : gene-EGK62_RS35690
product : pyocin S5
protein_id : WP_003112561.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271770/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSZ01000100.1 Protein Homology CDS 860 2053 . + 0 ID=cds-WP_003112561.1;Parent=gene-EGK62_RS35690;Dbxref=GenBank:WP_003112561.1;Name=WP_003112561.1;gbkey=CDS;gene=pyoS5;inference=COORDINATES: similar to AA sequence:RefSeq:WP_153570677.1;locus_tag=EGK62_RS35690;product=pyocin S5;protein_id=WP_003112561.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGK62_RS35695' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGK62_RS35695' for NZ_RHSZ01000100.1 Protein Homology CDS 2077 2346 -
dbxref : GenBank:WP_185957974.1
gbkey : CDS
id : cds-WP_185957974.1
inference : COORDINATES: protein motif:HMM:NF015489.5
locus_tag : EGK62_RS35695
name : WP_185957974.1
parent : gene-EGK62_RS35695
product : colicin E1 immunity protein
protein_id : WP_185957974.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271770/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSZ01000100.1 Protein Homology CDS 2078 2347 . - 0 ID=cds-WP_185957974.1;Parent=gene-EGK62_RS35695;Dbxref=GenBank:WP_185957974.1;Name=WP_185957974.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF015489.5;locus_tag=EGK62_RS35695;product=colicin E1 immunity protein;pr |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271771/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271771/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271771/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271771/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271771/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY939_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY939_RS00005' for NZ_RXTK01000001.1 Protein Homology CDS 0 198 -
dbxref : GenBank:WP_148104652.1
gbkey : CDS
id : cds-WP_148104652.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_014604111.1
locus_tag : DY939_RS00005
name : WP_148104652.1
parent : gene-DY939_RS00005
partial : true
product : hypothetical protein
protein_id : WP_148104652.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271771/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTK01000001.1 Protein Homology CDS 1 199 . - 0 ID=cds-WP_148104652.1;Parent=gene-DY939_RS00005;Dbxref=GenBank:WP_148104652.1;Name=WP_148104652.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014604111.1;locus_tag=DY939_RS00005;partial=true;product=hypothetical protein;protein_id=WP_148104652.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY939_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY939_RS00010' for NZ_RXTK01000001.1 Protein Homology CDS 213 1361 -
dbxref : GenBank:WP_023098865.1
gbkey : CDS
id : cds-WP_023098865.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_020750433.1
locus_tag : DY939_RS00010
name : WP_023098865.1
parent : gene-DY939_RS00010
product : DUF6531 domain-containing protein
protein_id : WP_023098865.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271771/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTK01000001.1 Protein Homology CDS 214 1362 . - 0 ID=cds-WP_023098865.1;Parent=gene-DY939_RS00010;Dbxref=GenBank:WP_023098865.1;Name=WP_023098865.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_020750433.1;locus_tag=DY939_RS00010;product=DUF6531 domain-containing protein;protein_id=WP_023098865.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY939_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY939_RS00015' for NZ_RXTK01000001.1 Protein Homology CDS 3327 4535 -
dbxref : GenBank:WP_003096105.1
gbkey : CDS
id : cds-WP_003096105.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_149411321.1
locus_tag : DY939_RS00015
name : WP_003096105.1
parent : gene-DY939_RS00015
product : tyrosine-type recombinase/integrase
protein_id : WP_003096105.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271771/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTK01000001.1 Protein Homology CDS 3328 4536 . - 0 ID=cds-WP_003096105.1;Parent=gene-DY939_RS00015;Dbxref=GenBank:WP_003096105.1;Name=WP_003096105.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:Re |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271772/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271772/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271772/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271772/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271772/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY930_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY930_RS00005' for NZ_RXTB01000001.1 Protein Homology CDS 92 1369 -
dbxref : GenBank:WP_003102247.1
gbkey : CDS
go_function : acyltransferase activity|0016746||IEA
id : cds-WP_003102247.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253473.1
locus_tag : DY930_RS00005
name : WP_003102247.1
ontology_term : GO:0016746
parent : gene-DY930_RS00005
product : acetyl-CoA C-acetyltransferase
protein_id : WP_003102247.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271772/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTB01000001.1 Protein Homology CDS 93 1370 . - 0 ID=cds-WP_003102247.1;Parent=gene-DY930_RS00005;Dbxref=GenBank:WP_003102247.1;Name=WP_003102247.1;Ontology_term=GO:0016746;gbkey=CDS;go_function=acyltransferase activity|0016746||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253473.1;locus_tag=DY930_RS00005;product=acetyl-CoA C-acetyltransferase;protein_id=WP_003102247.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY930_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY930_RS00010' for NZ_RXTB01000001.1 Protein Homology CDS 1624 2979 +
dbxref : GenBank:WP_023128464.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA
id : cds-WP_023128464.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253474.1
locus_tag : DY930_RS00010
name : WP_023128464.1
ontology_term : GO:0016491
parent : gene-DY930_RS00010
product : 3-oxoacyl-ACP reductase
protein_id : WP_023128464.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271772/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTB01000001.1 Protein Homology CDS 1625 2980 . + 0 ID=cds-WP_023128464.1;Parent=gene-DY930_RS00010;Dbxref=GenBank:WP_023128464.1;Name=WP_023128464.1;Ontology_term=GO:0016491;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253474.1;locus_tag=DY930_RS00010;product=3-oxoacyl-ACP reductase;protein_id=WP_023128464.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY930_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY930_RS00015' for NZ_RXTB01000001.1 Protein Homology CDS 3091 4092 -
dbxref : GenBank:WP_003095270.1
gbkey : CDS
go_function : DNA binding|0003677||IEA
go_process : regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003095270.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253475.1
locus_tag : DY930_RS00015
name : WP_003095270.1
ontology_term : GO:0006355,GO:0003677
parent : gene-DY930_RS00015
product : AraC family transcriptional regulator
protein_id : WP_003 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271773/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271773/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271773/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271773/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271773/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY948_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY948_RS00005' for NZ_RXTT01000001.1 Protein Homology CDS 29 637 -
dbxref : GenBank:WP_003095055.1
gbkey : CDS
gene : msrQ
id : cds-WP_003095055.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253379.1
locus_tag : DY948_RS00005
name : WP_003095055.1
parent : gene-DY948_RS00005
product : protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
protein_id : WP_003095055.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271773/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTT01000001.1 Protein Homology CDS 30 638 . - 0 ID=cds-WP_003095055.1;Parent=gene-DY948_RS00005;Dbxref=GenBank:WP_003095055.1;Name=WP_003095055.1;gbkey=CDS;gene=msrQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253379.1;locus_tag=DY948_RS00005;product=protein-methionine-sulfoxide reductase heme-binding subunit MsrQ;protein_id=WP_003095055.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY948_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY948_RS00010' for NZ_RXTT01000001.1 Protein Homology CDS 637 1650 -
dbxref : GenBank:WP_003095056.1
gbkey : CDS
gene : msrP
go_function : oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA
go_process : protein repair|0030091||IEA
id : cds-WP_003095056.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253380.1
locus_tag : DY948_RS00010
name : WP_003095056.1
ontology_term : GO:0030091,GO:0016667,GO:0043546
parent : gene-DY948_RS00010
product : protein-methionine-sulfoxide reductase catalytic subunit MsrP
protein_id : WP_003095056.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271773/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTT01000001.1 Protein Homology CDS 638 1651 . - 0 ID=cds-WP_003095056.1;Parent=gene-DY948_RS00010;Dbxref=GenBank:WP_003095056.1;Name=WP_003095056.1;Ontology_term=GO:0030091,GO:0016667,GO:0043546;gbkey=CDS;gene=msrP;go_function=oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA;go_process=protein repair|0030091||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253380.1;locus_tag=DY948_RS00010;product=protein-methionine-sulfoxide reductase catalytic subunit MsrP;protein_id=WP_003095056.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY948_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY948_RS00015' for NZ_RXTT01000001.1 Protein Homology CDS 1711 2526 -
dbxref : GenBank:WP_003095061.1
gbkey : CDS
gene : pssA
go_function : CDP-diacylglycerol-serine O-phosphat |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271774/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271774/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271774/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271774/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271774/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY952_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY952_RS00005' for NZ_RXTX01000001.1 Protein Homology CDS 322 3417 -
dbxref : GenBank:WP_096246817.1
gbkey : CDS
gene : dnaE2
id : cds-WP_096246817.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY952_RS00005
name : WP_096246817.1
parent : gene-DY952_RS00005
product : error-prone DNA polymerase
protein_id : WP_096246817.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271774/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTX01000001.1 Protein Homology CDS 323 3418 . - 0 ID=cds-WP_096246817.1;Parent=gene-DY952_RS00005;Dbxref=GenBank:WP_096246817.1;Name=WP_096246817.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY952_RS00005;product=error-prone DNA polymerase;protein_id=WP_096246817.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY952_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY952_RS00010' for NZ_RXTX01000001.1 Protein Homology CDS 3393 4808 -
dbxref : GenBank:WP_126569722.1
gbkey : CDS
id : cds-WP_126569722.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY952_RS00010
name : WP_126569722.1
parent : gene-DY952_RS00010
product : Y-family DNA polymerase
protein_id : WP_126569722.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271774/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTX01000001.1 Protein Homology CDS 3394 4809 . - 0 ID=cds-WP_126569722.1;Parent=gene-DY952_RS00010;Dbxref=GenBank:WP_126569722.1;Name=WP_126569722.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY952_RS00010;product=Y-family DNA polymerase;protein_id=WP_126569722.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY952_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY952_RS00015' for NZ_RXTX01000001.1 Protein Homology CDS 4816 5421 -
dbxref : GenBank:WP_031639058.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031639058.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_014820649.1
locus_tag : DY952_RS00015
name : WP_031639058.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY952_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031639058.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271774/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTX01000001.1 Protein Homology CDS 4817 5422 . - 0 ID=cds-WP_031639058.1;Parent=gene-DY952_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271775/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271775/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271775/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271775/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271775/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY979_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY979_RS00005' for NZ_RXUZ01000001.1 Protein Homology CDS 341 1312 +
dbxref : GenBank:WP_003096673.1
gbkey : CDS
gene : pstS
id : cds-WP_003096673.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254056.1
locus_tag : DY979_RS00005
name : WP_003096673.1
parent : gene-DY979_RS00005
product : phosphate ABC transporter substrate-binding protein PstS
protein_id : WP_003096673.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271775/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUZ01000001.1 Protein Homology CDS 342 1313 . + 0 ID=cds-WP_003096673.1;Parent=gene-DY979_RS00005;Dbxref=GenBank:WP_003096673.1;Name=WP_003096673.1;gbkey=CDS;gene=pstS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254056.1;locus_tag=DY979_RS00005;product=phosphate ABC transporter substrate-binding protein PstS;protein_id=WP_003096673.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY979_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY979_RS00010' for NZ_RXUZ01000001.1 Protein Homology CDS 1735 3768 +
dbxref : GenBank:WP_077688114.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_077688114.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254055.1
locus_tag : DY979_RS00010
name : WP_077688114.1
ontology_term : GO:0055085,GO:0016020
parent : gene-DY979_RS00010
product : ABC transporter permease subunit
protein_id : WP_077688114.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271775/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUZ01000001.1 Protein Homology CDS 1736 3769 . + 0 ID=cds-WP_077688114.1;Parent=gene-DY979_RS00010;Dbxref=GenBank:WP_077688114.1;Name=WP_077688114.1;Ontology_term=GO:0055085,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254055.1;locus_tag=DY979_RS00010;product=ABC transporter permease subunit;protein_id=WP_077688114.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY979_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY979_RS00015' for NZ_RXUZ01000001.1 Protein Homology CDS 3788 5464 +
dbxref : GenBank:WP_003096667.1
gbkey : CDS
gene : pstA
go_component : plasma membrane|0005886||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ATPase-coupled phosphate ion transmembrane transporter activity|0015415||IEA
go_process : phosphate ion transport|0006817||IEA
id : cds-WP_003096667.1
inference : COORDINATES: |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271776/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271776/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271776/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271776/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271776/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY995_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY995_RS00005' for NZ_RXVQ01000001.1 Protein Homology CDS 0 514 +
dbxref : GenBank:WP_148105496.1
gbkey : CDS
id : cds-WP_148105496.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003111978.1
locus_tag : DY995_RS00005
name : WP_148105496.1
parent : gene-DY995_RS00005
partial : true
product : RHS repeat-associated core domain-containing protein
protein_id : WP_148105496.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271776/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVQ01000001.1 Protein Homology CDS 1 515 . + 2 ID=cds-WP_148105496.1;Parent=gene-DY995_RS00005;Dbxref=GenBank:WP_148105496.1;Name=WP_148105496.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003111978.1;locus_tag=DY995_RS00005;partial=true;product=RHS repeat-associated core domain-containing protein;protein_id=WP_148105496.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY995_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY995_RS00010' for NZ_RXVQ01000001.1 GeneMarkS-2+ CDS 1155 1487 +
dbxref : GenBank:WP_023113110.1
gbkey : CDS
id : cds-WP_023113110.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY995_RS00010
name : WP_023113110.1
parent : gene-DY995_RS00010
product : hypothetical protein
protein_id : WP_023113110.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271776/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVQ01000001.1 GeneMarkS-2+ CDS 1156 1488 . + 0 ID=cds-WP_023113110.1;Parent=gene-DY995_RS00010;Dbxref=GenBank:WP_023113110.1;Name=WP_023113110.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY995_RS00010;product=hypothetical protein;protein_id=WP_023113110.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY995_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY995_RS00025' for NZ_RXVQ01000001.1 Protein Homology CDS 2573 3097 -
dbxref : GenBank:WP_003120098.1
gbkey : CDS
id : cds-WP_003120098.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251154.1
locus_tag : DY995_RS00025
name : WP_003120098.1
parent : gene-DY995_RS00025
product : hypothetical protein
protein_id : WP_003120098.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271776/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVQ01000001.1 Protein Homology CDS 2574 3098 . - 0 ID=cds-WP_003120098.1;Parent=gene-DY995_RS00025;Dbxref=GenBank:WP_003120098.1;Name=WP_003120098.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_25115 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271777/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271777/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271777/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271777/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271777/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY983_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY983_RS00010' for NZ_RXVD01000001.1 Protein Homology CDS 751 1239 -
dbxref : GenBank:WP_003115119.1
gbkey : CDS
gene : phzB
id : cds-WP_003115119.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250591.1
locus_tag : DY983_RS00010
name : WP_003115119.1
parent : gene-DY983_RS00010
product : phenazine biosynthesis protein PhzB
protein_id : WP_003115119.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271777/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVD01000001.1 Protein Homology CDS 752 1240 . - 0 ID=cds-WP_003115119.1;Parent=gene-DY983_RS00010;Dbxref=GenBank:WP_003115119.1;Name=WP_003115119.1;gbkey=CDS;gene=phzB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250591.1;locus_tag=DY983_RS00010;product=phenazine biosynthesis protein PhzB;protein_id=WP_003115119.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY983_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY983_RS00015' for NZ_RXVD01000001.1 Protein Homology CDS 1275 1763 -
dbxref : GenBank:WP_003117657.1
gbkey : CDS
gene : phzA
id : cds-WP_003117657.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250590.1
locus_tag : DY983_RS00015
name : WP_003117657.1
parent : gene-DY983_RS00015
product : phenazine biosynthesis protein PhzA
protein_id : WP_003117657.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271777/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVD01000001.1 Protein Homology CDS 1276 1764 . - 0 ID=cds-WP_003117657.1;Parent=gene-DY983_RS00015;Dbxref=GenBank:WP_003117657.1;Name=WP_003117657.1;gbkey=CDS;gene=phzA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250590.1;locus_tag=DY983_RS00015;product=phenazine biosynthesis protein PhzA;protein_id=WP_003117657.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY983_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY983_RS00020' for NZ_RXVD01000001.1 Protein Homology CDS 2245 2958 -
dbxref : GenBank:WP_003118960.1
gbkey : CDS
gene : qscR
id : cds-WP_003118960.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250589.1
locus_tag : DY983_RS00020
name : WP_003118960.1
parent : gene-DY983_RS00020
product : quorum-sensing transcriptional repressor QscR
protein_id : WP_003118960.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271777/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXVD01000001.1 Protein Homology CDS 2246 2959 . - 0 ID=cds-WP_003118960.1;Parent=gene-DY983_RS00020;Dbxref=GenBank:WP_003118960.1;Name=WP_003118960.1;gbkey=CDS;gene=qscR; |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271778/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271778/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271778/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271778/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271778/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY981_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY981_RS00005' for NZ_RXVB01000001.1 Protein Homology CDS 0 694 +
dbxref : GenBank:WP_260478539.1
gbkey : CDS
go_function : phosphorelay sensor kinase activity|0000155||IEA,ATP binding|0005524||IEA
id : cds-WP_260478539.1
inference : COORDINATES: protein motif:HMM:NF024970.5
locus_tag : DY981_RS00005
name : WP_260478539.1
ontology_term : GO:0000155,GO:0005524
parent : gene-DY981_RS00005
partial : true
product : sensor histidine kinase
protein_id : WP_260478539.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271778/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVB01000001.1 Protein Homology CDS 1 695 . + 2 ID=cds-WP_260478539.1;Parent=gene-DY981_RS00005;Dbxref=GenBank:WP_260478539.1;Name=WP_260478539.1;Ontology_term=GO:0000155,GO:0005524;gbkey=CDS;go_function=phosphorelay sensor kinase activity|0000155||IEA,ATP binding|0005524||IEA;inference=COORDINATES: protein motif:HMM:NF024970.5;locus_tag=DY981_RS00005;partial=true;product=sensor histidine kinase;protein_id=WP_260478539.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY981_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY981_RS00010' for NZ_RXVB01000001.1 Protein Homology CDS 691 1377 +
dbxref : GenBank:WP_126621679.1
gbkey : CDS
go_process : phosphorelay signal transduction system|0000160||IEA
id : cds-WP_126621679.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_008175410.1
locus_tag : DY981_RS00010
name : WP_126621679.1
ontology_term : GO:0000160
parent : gene-DY981_RS00010
product : response regulator
protein_id : WP_126621679.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271778/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVB01000001.1 Protein Homology CDS 692 1378 . + 0 ID=cds-WP_126621679.1;Parent=gene-DY981_RS00010;Dbxref=GenBank:WP_126621679.1;Name=WP_126621679.1;Ontology_term=GO:0000160;gbkey=CDS;go_process=phosphorelay signal transduction system|0000160||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008175410.1;locus_tag=DY981_RS00010;product=response regulator;protein_id=WP_126621679.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY981_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY981_RS00015' for NZ_RXVB01000001.1 Protein Homology CDS 1451 1705 -
dbxref : GenBank:WP_221768699.1
gbkey : CDS
go_function : ATP binding|0005524||IEA,kinase activity|0016301||IEA
go_process : phosphorylation|0016310||IEA
id : cds-WP_221768699.1
inference : COORDINATES: protein motif:HMM:NF013491.5
locus_tag : DY981_RS00015
name : WP_221768699.1
ontology_te |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271779/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271779/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271779/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271779/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271779/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY951_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY951_RS00005' for NZ_RXTW01000001.1 Protein Homology CDS 342 1313 +
dbxref : GenBank:WP_003096673.1
gbkey : CDS
gene : pstS
id : cds-WP_003096673.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254056.1
locus_tag : DY951_RS00005
name : WP_003096673.1
parent : gene-DY951_RS00005
product : phosphate ABC transporter substrate-binding protein PstS
protein_id : WP_003096673.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271779/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTW01000001.1 Protein Homology CDS 343 1314 . + 0 ID=cds-WP_003096673.1;Parent=gene-DY951_RS00005;Dbxref=GenBank:WP_003096673.1;Name=WP_003096673.1;gbkey=CDS;gene=pstS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254056.1;locus_tag=DY951_RS00005;product=phosphate ABC transporter substrate-binding protein PstS;protein_id=WP_003096673.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY951_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY951_RS00010' for NZ_RXTW01000001.1 Protein Homology CDS 1736 3769 +
dbxref : GenBank:WP_003123734.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003123734.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254055.1
locus_tag : DY951_RS00010
name : WP_003123734.1
ontology_term : GO:0055085,GO:0016020
parent : gene-DY951_RS00010
product : ABC transporter permease subunit
protein_id : WP_003123734.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271779/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTW01000001.1 Protein Homology CDS 1737 3770 . + 0 ID=cds-WP_003123734.1;Parent=gene-DY951_RS00010;Dbxref=GenBank:WP_003123734.1;Name=WP_003123734.1;Ontology_term=GO:0055085,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254055.1;locus_tag=DY951_RS00010;product=ABC transporter permease subunit;protein_id=WP_003123734.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY951_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY951_RS00015' for NZ_RXTW01000001.1 Protein Homology CDS 3789 5465 +
dbxref : GenBank:WP_003096667.1
gbkey : CDS
gene : pstA
go_component : plasma membrane|0005886||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ATPase-coupled phosphate ion transmembrane transporter activity|0015415||IEA
go_process : phosphate ion transport|0006817||IEA
id : cds-WP_003096667.1
inference : COORDINATES: |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271780/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271780/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271780/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271780/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271780/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY956_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY956_RS00010' for NZ_RXUB01000001.1 Protein Homology CDS 213 1064 +
dbxref : GenBank:WP_003157409.1
gbkey : CDS
go_function : carbohydrate binding|0030246||IEA,glucose-6-phosphate 1-epimerase activity|0047938||IEA
go_process : carbohydrate metabolic process|0005975||IEA
id : cds-WP_003157409.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1
locus_tag : DY956_RS00010
name : WP_003157409.1
ontology_term : GO:0005975,GO:0030246,GO:0047938
parent : gene-DY956_RS00010
product : D-hexose-6-phosphate mutarotase
protein_id : WP_003157409.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271780/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUB01000001.1 Protein Homology CDS 214 1065 . + 0 ID=cds-WP_003157409.1;Parent=gene-DY956_RS00010;Dbxref=GenBank:WP_003157409.1;Name=WP_003157409.1;Ontology_term=GO:0005975,GO:0030246,GO:0047938;gbkey=CDS;go_function=carbohydrate binding|0030246||IEA,glucose-6-phosphate 1-epimerase activity|0047938||IEA;go_process=carbohydrate metabolic process|0005975||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1;locus_tag=DY956_RS00010;product=D-hexose-6-phosphate mutarotase;protein_id=WP_003157409.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY956_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY956_RS00015' for NZ_RXUB01000001.1 Protein Homology CDS 1073 1930 -
dbxref : GenBank:WP_034078349.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA,carbohydrate derivative binding|0097367||IEA
go_process : DNA-templated transcription|0006351||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_034078349.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251874.1
locus_tag : DY956_RS00015
name : WP_034078349.1
ontology_term : GO:0006351,GO:0006355,GO:0003677,GO:0003700,GO:0097367
parent : gene-DY956_RS00015
product : MurR/RpiR family transcriptional regulator
protein_id : WP_034078349.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271780/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUB01000001.1 Protein Homology CDS 1074 1931 . - 0 ID=cds-WP_034078349.1;Parent=gene-DY956_RS00015;Dbxref=GenBank:WP_034078349.1;Name=WP_034078349.1;Ontology_term=GO:0006351,GO:0006355,GO:0003677,GO:0003700,GO:0097367;gbkey=CDS;go_function=DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA,carbohydrate derivative binding|0097367||IEA;go_process=DNA-templated transcription|0006351||IEA,regulation of DNA-templated transcription|0006355||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_25 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271781/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271781/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271781/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271781/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271781/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY965_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY965_RS00005' for NZ_RXUK01000001.1 Protein Homology CDS 35 523 -
dbxref : GenBank:WP_003123955.1
gbkey : CDS
gene : phzB
id : cds-WP_003123955.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252900.1
locus_tag : DY965_RS00005
name : WP_003123955.1
parent : gene-DY965_RS00005
product : phenazine biosynthesis protein PhzB
protein_id : WP_003123955.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271781/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUK01000001.1 Protein Homology CDS 36 524 . - 0 ID=cds-WP_003123955.1;Parent=gene-DY965_RS00005;Dbxref=GenBank:WP_003123955.1;Name=WP_003123955.1;gbkey=CDS;gene=phzB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252900.1;locus_tag=DY965_RS00005;product=phenazine biosynthesis protein PhzB;protein_id=WP_003123955.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY965_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY965_RS00010' for NZ_RXUK01000001.1 Protein Homology CDS 553 1041 -
dbxref : GenBank:WP_003118957.1
gbkey : CDS
gene : phzA
id : cds-WP_003118957.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252899.1
locus_tag : DY965_RS00010
name : WP_003118957.1
parent : gene-DY965_RS00010
product : phenazine biosynthesis protein PhzA
protein_id : WP_003118957.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271781/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUK01000001.1 Protein Homology CDS 554 1042 . - 0 ID=cds-WP_003118957.1;Parent=gene-DY965_RS00010;Dbxref=GenBank:WP_003118957.1;Name=WP_003118957.1;gbkey=CDS;gene=phzA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252899.1;locus_tag=DY965_RS00010;product=phenazine biosynthesis protein PhzA;protein_id=WP_003118957.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY965_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY965_RS00020' for NZ_RXUK01000001.1 Protein Homology CDS 1738 2742 +
dbxref : GenBank:WP_016852432.1
gbkey : CDS
gene : phzM
id : cds-WP_016852432.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252898.1
locus_tag : DY965_RS00020
name : WP_016852432.1
parent : gene-DY965_RS00020
product : phenazine-1-carboxylate N-methyltransferase PhzM
protein_id : WP_016852432.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271781/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUK01000001.1 Protein Homology CDS 1739 2743 . + 0 ID=cds-WP_016852432.1;Parent=gene-DY965_RS00020;Dbxref=GenBank:WP_016852432.1;Name=WP_016852432.1;gbkey=CDS;gene=phzM;infe |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271782/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271782/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271782/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271782/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271782/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY970_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY970_RS00005' for NZ_RXUP01000001.1 Protein Homology CDS 0 110 -
dbxref : GenBank:WP_221768115.1
gbkey : CDS
id : cds-WP_221768115.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003153496.1
locus_tag : DY970_RS00005
name : WP_221768115.1
parent : gene-DY970_RS00005
partial : true
product : PsiF family protein
protein_id : WP_221768115.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271782/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUP01000001.1 Protein Homology CDS 1 111 . - 0 ID=cds-WP_221768115.1;Parent=gene-DY970_RS00005;Dbxref=GenBank:WP_221768115.1;Name=WP_221768115.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003153496.1;locus_tag=DY970_RS00005;partial=true;product=PsiF family protein;protein_id=WP_221768115.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY970_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY970_RS00010' for NZ_RXUP01000001.1 Protein Homology CDS 265 804 +
dbxref : GenBank:WP_003095483.1
gbkey : CDS
go_function : catalytic activity|0003824||IEA,molybdopterin cofactor binding|0043546||IEA
id : cds-WP_003095483.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009877163.1
locus_tag : DY970_RS00010
name : WP_003095483.1
ontology_term : GO:0003824,GO:0043546
parent : gene-DY970_RS00010
product : MOSC domain-containing protein
protein_id : WP_003095483.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271782/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUP01000001.1 Protein Homology CDS 266 805 . + 0 ID=cds-WP_003095483.1;Parent=gene-DY970_RS00010;Dbxref=GenBank:WP_003095483.1;Name=WP_003095483.1;Ontology_term=GO:0003824,GO:0043546;gbkey=CDS;go_function=catalytic activity|0003824||IEA,molybdopterin cofactor binding|0043546||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009877163.1;locus_tag=DY970_RS00010;product=MOSC domain-containing protein;protein_id=WP_003095483.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY970_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY970_RS00015' for NZ_RXUP01000001.1 Protein Homology CDS 893 1237 +
dbxref : GenBank:WP_003095488.1
gbkey : CDS
gene : osmE
go_component : outer membrane|0019867||IEA
id : cds-WP_003095488.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253563.1
locus_tag : DY970_RS00015
name : WP_003095488.1
ontology_term : GO:0019867
parent : gene-DY970_RS00015
product : osmotically-inducible lipoprotein OsmE
protein_id : WP_003095488.1
source : Protein Homology
transl_table : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271783/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271783/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271783/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271783/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271783/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA25_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA25_RS00015' for NZ_RXUW01000001.1 Protein Homology CDS 890 1972 -
dbxref : GenBank:WP_044727243.1
gbkey : CDS
go_function : nucleotide binding|0000166||IEA
id : cds-WP_044727243.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253836.1
locus_tag : DZA25_RS00015
name : WP_044727243.1
ontology_term : GO:0000166
parent : gene-DZA25_RS00015
product : oxidoreductase
protein_id : WP_044727243.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271783/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RXUW01000001.1 Protein Homology CDS 891 1973 . - 0 ID=cds-WP_044727243.1;Parent=gene-DZA25_RS00015;Dbxref=GenBank:WP_044727243.1;Name=WP_044727243.1;Ontology_term=GO:0000166;gbkey=CDS;go_function=nucleotide binding|0000166||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253836.1;locus_tag=DZA25_RS00015;product=oxidoreductase;protein_id=WP_044727243.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA25_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA25_RS00020' for NZ_RXUW01000001.1 Protein Homology CDS 2000 2272 -
dbxref : GenBank:WP_003096100.1
gbkey : CDS
go_function : iron ion binding|0005506||IEA
id : cds-WP_003096100.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253835.1
locus_tag : DZA25_RS00020
name : WP_003096100.1
ontology_term : GO:0005506
parent : gene-DZA25_RS00020
product : oxidative damage protection protein
protein_id : WP_003096100.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271783/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 19 'NZ_RXUW01000001.1 Protein Homology CDS 2001 2273 . - 0 ID=cds-WP_003096100.1;Parent=gene-DZA25_RS00020;Dbxref=GenBank:WP_003096100.1;Name=WP_003096100.1;Ontology_term=GO:0005506;gbkey=CDS;go_function=iron ion binding|0005506||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253835.1;locus_tag=DZA25_RS00020;product=oxidative damage protection protein;protein_id=WP_003096100.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA25_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA25_RS00025' for NZ_RXUW01000001.1 Protein Homology CDS 2316 3383 -
dbxref : GenBank:WP_003096098.1
gbkey : CDS
gene : mutY
go_function : DNA N-glycosylase activity|0019104||IEA
go_process : DNA repair|0006281||IEA
id : cds-WP_003096098.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253834.1
locus_tag : DZA25_RS00025
name : WP_003096098.1
ontology_term : GO:0006281,GO:0019104
parent : gene-DZA25_RS00025
product : A/G-specific adenine glycosylase
protein_id : WP_003096098.1
source : Protein Homolo |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271784/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271784/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271784/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271784/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271784/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY971_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY971_RS00005' for NZ_RXUQ01000001.1 Protein Homology CDS 0 1260 -
dbxref : GenBank:WP_126550699.1
gbkey : CDS
go_function : CTP synthase activity|0003883||IEA
go_process : pyrimidine nucleotide biosynthetic process|0006221||IEA,CTP biosynthetic process|0006241||IEA
id : cds-WP_126550699.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252327.1
locus_tag : DY971_RS00005
name : WP_126550699.1
ontology_term : GO:0006221,GO:0006241,GO:0003883
parent : gene-DY971_RS00005
partial : true
product : CTP synthase
protein_id : WP_126550699.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271784/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUQ01000001.1 Protein Homology CDS 1 1261 . - 0 ID=cds-WP_126550699.1;Parent=gene-DY971_RS00005;Dbxref=GenBank:WP_126550699.1;Name=WP_126550699.1;Ontology_term=GO:0006221,GO:0006241,GO:0003883;gbkey=CDS;go_function=CTP synthase activity|0003883||IEA;go_process=pyrimidine nucleotide biosynthetic process|0006221||IEA,CTP biosynthetic process|0006241||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252327.1;locus_tag=DY971_RS00005;partial=true;product=CTP synthase;protein_id=WP_126550699.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY971_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY971_RS00010' for NZ_RXUQ01000001.1 Protein Homology CDS 1431 2759 -
dbxref : GenBank:WP_049951332.1
gbkey : CDS
gene : tilS
go_function : nucleotide binding|0000166||IEA,ATP binding|0005524||IEA,ligase activity%2C forming carbon-nitrogen bonds|0016879||IEA
go_process : tRNA processing|0008033||IEA
id : cds-WP_049951332.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252328.1
locus_tag : DY971_RS00010
name : WP_049951332.1
ontology_term : GO:0008033,GO:0000166,GO:0005524,GO:0016879
parent : gene-DY971_RS00010
product : tRNA lysidine(34) synthetase TilS
protein_id : WP_049951332.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271784/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUQ01000001.1 Protein Homology CDS 1432 2760 . - 0 ID=cds-WP_049951332.1;Parent=gene-DY971_RS00010;Dbxref=GenBank:WP_049951332.1;Name=WP_049951332.1;Ontology_term=GO:0008033,GO:0000166,GO:0005524,GO:0016879;gbkey=CDS;gene=tilS;go_function=nucleotide binding|0000166||IEA,ATP binding|0005524||IEA,ligase activity%2C forming carbon-nitrogen bonds|0016879||IEA;go_process=tRNA processing|0008033||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252328.1;locus_tag=DY971_RS00010;product=tRNA lysidine(34) synthetase TilS;protein_id=WP_049951332.1;transl_table=11'
WARNING_TRANSCRIPT_NO |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271785/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271785/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271785/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271785/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271785/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY931_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY931_RS00010' for NZ_RXTC01000001.1 Protein Homology CDS 242 1123 +
dbxref : GenBank:WP_033937931.1
gbkey : CDS
id : cds-WP_033937931.1
inference : COORDINATES: protein motif:HMM:NF024894.5
locus_tag : DY931_RS00010
name : WP_033937931.1
parent : gene-DY931_RS00010
product : DUF4123 domain-containing protein
protein_id : WP_033937931.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271785/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTC01000001.1 Protein Homology CDS 243 1124 . + 0 ID=cds-WP_033937931.1;Parent=gene-DY931_RS00010;Dbxref=GenBank:WP_033937931.1;Name=WP_033937931.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024894.5;locus_tag=DY931_RS00010;product=DUF4123 domain-containing protein;protein_id=WP_033937931.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY931_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY931_RS00015' for NZ_RXTC01000001.1 Protein Homology CDS 1120 4644 +
dbxref : GenBank:WP_033937927.1
gbkey : CDS
id : cds-WP_033937927.1
inference : COORDINATES: protein motif:HMM:NF042700.3
locus_tag : DY931_RS00015
name : WP_033937927.1
parent : gene-DY931_RS00015
product : toxin VasX
protein_id : WP_033937927.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271785/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTC01000001.1 Protein Homology CDS 1121 4645 . + 0 ID=cds-WP_033937927.1;Parent=gene-DY931_RS00015;Dbxref=GenBank:WP_033937927.1;Name=WP_033937927.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF042700.3;locus_tag=DY931_RS00015;product=toxin VasX;protein_id=WP_033937927.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY931_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY931_RS00020' for NZ_RXTC01000001.1 Protein Homology CDS 4628 5770 +
dbxref : GenBank:WP_223724265.1
gbkey : CDS
id : cds-WP_223724265.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_020289231.1
locus_tag : DY931_RS00020
name : WP_223724265.1
parent : gene-DY931_RS00020
product : hypothetical protein
protein_id : WP_223724265.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271785/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXTC01000001.1 Protein Homology CDS 4629 5771 . + 0 ID=cds-WP_223724265.1;Parent=gene-DY931_RS00020;Dbxref=GenBank:WP_223724265.1;Name=WP_223724265.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_020289231.1;locus_tag=DY931_RS00020;product=hypothetical protein;protein_id=WP_223724265.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'ge |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271786/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271786/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271786/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271786/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271786/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY943_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY943_RS00005' for NZ_RXTO01000001.1 Protein Homology CDS 0 1039 -
dbxref : GenBank:WP_148104789.1
gbkey : CDS
id : cds-WP_148104789.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_011002530.1
locus_tag : DY943_RS00005
name : WP_148104789.1
parent : gene-DY943_RS00005
partial : true
product : AAA family ATPase
protein_id : WP_148104789.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271786/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTO01000001.1 Protein Homology CDS 1 1040 . - 0 ID=cds-WP_148104789.1;Parent=gene-DY943_RS00005;Dbxref=GenBank:WP_148104789.1;Name=WP_148104789.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_011002530.1;locus_tag=DY943_RS00005;partial=true;product=AAA family ATPase;protein_id=WP_148104789.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY943_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY943_RS00010' for NZ_RXTO01000001.1 Protein Homology CDS 1585 2412 +
dbxref : GenBank:WP_003092327.1
gbkey : CDS
id : cds-WP_003092327.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012638432.1
locus_tag : DY943_RS00010
name : WP_003092327.1
parent : gene-DY943_RS00010
product : DUF932 domain-containing protein
protein_id : WP_003092327.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271786/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTO01000001.1 Protein Homology CDS 1586 2413 . + 0 ID=cds-WP_003092327.1;Parent=gene-DY943_RS00010;Dbxref=GenBank:WP_003092327.1;Name=WP_003092327.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012638432.1;locus_tag=DY943_RS00010;product=DUF932 domain-containing protein;protein_id=WP_003092327.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY943_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY943_RS00015' for NZ_RXTO01000001.1 Protein Homology CDS 2493 4562 +
dbxref : GenBank:WP_000994919.1
gbkey : CDS
id : cds-WP_000994919.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_000994919.1
locus_tag : DY943_RS00015
name : WP_000994919.1
parent : gene-DY943_RS00015
product : ParB/RepB/Spo0J family partition protein
protein_id : WP_000994919.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271786/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTO01000001.1 Protein Homology CDS 2494 4563 . + 0 ID=cds-WP_000994919.1;Parent=gene-DY943_RS00015;Dbxref=GenBank:WP_000994919.1;Name=WP_000994919.1;gbkey=CDS;inference=COORDINATES: similar to AA sequen |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271787/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271787/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271787/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271787/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271787/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY929_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY929_RS00005' for NZ_RXTA01000001.1 Protein Homology CDS 0 645 +
dbxref : GenBank:WP_148105117.1
gbkey : CDS
id : cds-WP_148105117.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012638432.1
locus_tag : DY929_RS00005
name : WP_148105117.1
parent : gene-DY929_RS00005
partial : true
product : DUF932 domain-containing protein
protein_id : WP_148105117.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271787/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTA01000001.1 Protein Homology CDS 1 646 . + 1 ID=cds-WP_148105117.1;Parent=gene-DY929_RS00005;Dbxref=GenBank:WP_148105117.1;Name=WP_148105117.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012638432.1;locus_tag=DY929_RS00005;partial=true;product=DUF932 domain-containing protein;protein_id=WP_148105117.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY929_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY929_RS00010' for NZ_RXTA01000001.1 Protein Homology CDS 725 2776 +
dbxref : GenBank:WP_016851781.1
gbkey : CDS
id : cds-WP_016851781.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_011516017.1
locus_tag : DY929_RS00010
name : WP_016851781.1
parent : gene-DY929_RS00010
product : ParB/RepB/Spo0J family partition protein
protein_id : WP_016851781.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271787/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTA01000001.1 Protein Homology CDS 726 2777 . + 0 ID=cds-WP_016851781.1;Parent=gene-DY929_RS00010;Dbxref=GenBank:WP_016851781.1;Name=WP_016851781.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_011516017.1;locus_tag=DY929_RS00010;product=ParB/RepB/Spo0J family partition protein;protein_id=WP_016851781.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY929_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY929_RS00015' for NZ_RXTA01000001.1 Protein Homology CDS 2839 3048 +
dbxref : GenBank:WP_016851780.1
gbkey : CDS
id : cds-WP_016851780.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_008643223.1
locus_tag : DY929_RS00015
name : WP_016851780.1
parent : gene-DY929_RS00015
product : hypothetical protein
protein_id : WP_016851780.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271787/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTA01000001.1 Protein Homology CDS 2840 3049 . + 0 ID=cds-WP_016851780.1;Parent=gene-DY929_RS00015;Dbxref=GenBank:WP_016851780.1;Name=WP_016851780.1;gbkey=CDS;inference=COORDINATES: s |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271788/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271788/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271788/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271788/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271788/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY942_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY942_RS00005' for NZ_RXTN01000001.1 Protein Homology CDS 0 873 +
dbxref : GenBank:WP_143483724.1
gbkey : CDS
id : cds-WP_143483724.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252176.1
locus_tag : DY942_RS00005
name : WP_143483724.1
parent : gene-DY942_RS00005
partial : true
product : bacteriophage T4 gp5 trimerisation domain-containing protein
protein_id : WP_143483724.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271788/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTN01000001.1 Protein Homology CDS 1 874 . + 1 ID=cds-WP_143483724.1;Parent=gene-DY942_RS00005;Dbxref=GenBank:WP_143483724.1;Name=WP_143483724.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252176.1;locus_tag=DY942_RS00005;partial=true;product=bacteriophage T4 gp5 trimerisation domain-containing protein;protein_id=WP_143483724.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY942_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY942_RS00010' for NZ_RXTN01000001.1 Protein Homology CDS 877 4176 +
dbxref : GenBank:WP_003092035.1
gbkey : CDS
gene : pldA
id : cds-WP_003092035.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252177.1
locus_tag : DY942_RS00010
name : WP_003092035.1
parent : gene-DY942_RS00010
product : phospholipase D
protein_id : WP_003092035.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271788/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTN01000001.1 Protein Homology CDS 878 4177 . + 0 ID=cds-WP_003092035.1;Parent=gene-DY942_RS00010;Dbxref=GenBank:WP_003092035.1;Name=WP_003092035.1;gbkey=CDS;gene=pldA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252177.1;locus_tag=DY942_RS00010;product=phospholipase D;protein_id=WP_003092035.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY942_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY942_RS00015' for NZ_RXTN01000001.1 Protein Homology CDS 4605 5303 +
dbxref : GenBank:WP_003109999.1
gbkey : CDS
id : cds-WP_003109999.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003109999.1
locus_tag : DY942_RS00015
name : WP_003109999.1
parent : gene-DY942_RS00015
product : T6SS immunity protein Tli4 family protein
protein_id : WP_003109999.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271788/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTN01000001.1 Protein Homology CDS 4606 5304 . + 0 ID=cds-WP_003109999.1;Parent=gene-DY942_RS00015;Dbxref=GenBank:WP_003109999.1;Name=WP_0 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271789/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271789/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271789/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271789/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271789/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY945_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY945_RS00010' for NZ_RXTQ01000001.1 Protein Homology CDS 216 1067 +
dbxref : GenBank:WP_003112064.1
gbkey : CDS
id : cds-WP_003112064.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1
locus_tag : DY945_RS00010
name : WP_003112064.1
parent : gene-DY945_RS00010
product : D-hexose-6-phosphate mutarotase
protein_id : WP_003112064.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271789/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTQ01000001.1 Protein Homology CDS 217 1068 . + 0 ID=cds-WP_003112064.1;Parent=gene-DY945_RS00010;Dbxref=GenBank:WP_003112064.1;Name=WP_003112064.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1;locus_tag=DY945_RS00010;product=D-hexose-6-phosphate mutarotase;protein_id=WP_003112064.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY945_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY945_RS00015' for NZ_RXTQ01000001.1 Protein Homology CDS 1076 1933 -
dbxref : GenBank:WP_003091466.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA,carbohydrate derivative binding|0097367||IEA
go_process : DNA-templated transcription|0006351||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003091466.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251874.1
locus_tag : DY945_RS00015
name : WP_003091466.1
ontology_term : GO:0006351,GO:0006355,GO:0003677,GO:0003700,GO:0097367
parent : gene-DY945_RS00015
product : MurR/RpiR family transcriptional regulator
protein_id : WP_003091466.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271789/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTQ01000001.1 Protein Homology CDS 1077 1934 . - 0 ID=cds-WP_003091466.1;Parent=gene-DY945_RS00015;Dbxref=GenBank:WP_003091466.1;Name=WP_003091466.1;Ontology_term=GO:0006351,GO:0006355,GO:0003677,GO:0003700,GO:0097367;gbkey=CDS;go_function=DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA,carbohydrate derivative binding|0097367||IEA;go_process=DNA-templated transcription|0006351||IEA,regulation of DNA-templated transcription|0006355||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251874.1;locus_tag=DY945_RS00015;product=MurR/RpiR family transcriptional regulator;protein_id=WP_003091466.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY945_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY945_RS00020' for NZ_RXTQ01000001.1 Protein Homology CDS 2120 3589 +
dbxref : GenBank:WP_003091465.1
gbkey : CDS
gene : zwf
go_function : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271790/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271790/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271790/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271790/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271790/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY934_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY934_RS00005' for NZ_RXTF01000001.1 Protein Homology CDS 0 1409 -
dbxref : GenBank:WP_260472885.1
gbkey : CDS
id : cds-WP_260472885.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003162845.1
locus_tag : DY934_RS00005
name : WP_260472885.1
parent : gene-DY934_RS00005
partial : true
product : DUF6531 domain-containing protein
protein_id : WP_260472885.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271790/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTF01000001.1 Protein Homology CDS 1 1410 . - 0 ID=cds-WP_260472885.1;Parent=gene-DY934_RS00005;Dbxref=GenBank:WP_260472885.1;Name=WP_260472885.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003162845.1;locus_tag=DY934_RS00005;partial=true;product=DUF6531 domain-containing protein;protein_id=WP_260472885.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY934_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY934_RS00015' for NZ_RXTF01000001.1 Protein Homology CDS 2874 3419 +
dbxref : GenBank:WP_033982345.1
gbkey : CDS
go_function : N-acetyltransferase activity|0008080||IEA,acyltransferase activity|0016746||IEA
id : cds-WP_033982345.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003098709.1
locus_tag : DY934_RS00015
name : WP_033982345.1
ontology_term : GO:0008080,GO:0016746
parent : gene-DY934_RS00015
product : GNAT family N-acetyltransferase
protein_id : WP_033982345.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271790/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RXTF01000001.1 Protein Homology CDS 2875 3420 . + 0 ID=cds-WP_033982345.1;Parent=gene-DY934_RS00015;Dbxref=GenBank:WP_033982345.1;Name=WP_033982345.1;Ontology_term=GO:0008080,GO:0016746;gbkey=CDS;go_function=N-acetyltransferase activity|0008080||IEA,acyltransferase activity|0016746||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003098709.1;locus_tag=DY934_RS00015;product=GNAT family N-acetyltransferase;protein_id=WP_033982345.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY934_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY934_RS00020' for NZ_RXTF01000001.1 Protein Homology CDS 3585 3863 +
dbxref : GenBank:WP_033982428.1
gbkey : CDS
id : cds-WP_033982428.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252059.1
locus_tag : DY934_RS00020
name : WP_033982428.1
parent : gene-DY934_RS00020
product : hypothetical protein
protein_id : WP_033982428.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271790/wo |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271791/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271791/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271791/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271791/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271791/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY941_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY941_RS00010' for NZ_RXTM01000001.1 Protein Homology CDS 190 1005 +
dbxref : GenBank:WP_003107607.1
gbkey : CDS
id : cds-WP_003107607.1
inference : COORDINATES: protein motif:HMM:NF024894.5
locus_tag : DY941_RS00010
name : WP_003107607.1
parent : gene-DY941_RS00010
product : DUF4123 domain-containing protein
protein_id : WP_003107607.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271791/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTM01000001.1 Protein Homology CDS 191 1006 . + 0 ID=cds-WP_003107607.1;Parent=gene-DY941_RS00010;Dbxref=GenBank:WP_003107607.1;Name=WP_003107607.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024894.5;locus_tag=DY941_RS00010;product=DUF4123 domain-containing protein;protein_id=WP_003107607.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY941_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY941_RS00015' for NZ_RXTM01000001.1 Protein Homology CDS 1002 1523 +
dbxref : GenBank:WP_004351092.1
gbkey : CDS
id : cds-WP_004351092.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_004351092.1
locus_tag : DY941_RS00015
name : WP_004351092.1
parent : gene-DY941_RS00015
product : DUF3304 domain-containing protein
protein_id : WP_004351092.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271791/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTM01000001.1 Protein Homology CDS 1003 1524 . + 0 ID=cds-WP_004351092.1;Parent=gene-DY941_RS00015;Dbxref=GenBank:WP_004351092.1;Name=WP_004351092.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004351092.1;locus_tag=DY941_RS00015;product=DUF3304 domain-containing protein;protein_id=WP_004351092.1;transl_table=11'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_RXTM01000001.1:1-181) does not include 'gene-DY941_RS35865' (NZ_RXTM01000002.1:1-223). Created new gene 'null.2' (NZ_RXTM01000002.1:1-223). File '/jetstream2/scratch/main/jobs/72271791/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 20 'NZ_RXTM01000002.1 RefSeq pseudogene 1 223 . + . ID=gene-DY941_RS35865;Name=DY941_RS35865;gbkey=Gene;gene_biotype=pseudogene;locus_tag=DY941_RS35865;old_locus_tag=DY941_00020;partial=true;pseudo=true;start_range=.,1'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY941_RS35870' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY941_RS35870' for NZ_RXTM01000002.1 Protein Homology CDS 219 422 +
dbxref : GenBank:WP_071543491.1
gbkey : CDS
id : cds-WP_071543491.1
inference : COORDINATES: protein motif:HMM:NF023173.5
locus_tag : DY941_RS35870
name : WP_071543491.1
parent : gene-DY941_RS35870
product : DUF3304 domain-containing pr |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271792/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271792/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271792/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271792/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271792/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM490_RS00775' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM490_RS00775' for NZ_CP032257.1 Protein Homology CDS 738 1247 -
dbxref : GenBank:WP_003107976.1
gbkey : CDS
go_function : DNA-binding transcription factor activity|0003700||IEA,sigma factor activity|0016987||IEA
go_process : DNA-templated transcription initiation|0006352||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003107976.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250783.1
locus_tag : AM490_RS00775
name : WP_003107976.1
ontology_term : GO:0006352,GO:0006355,GO:0003700,GO:0016987
parent : gene-AM490_RS00775
product : sigma-70 family RNA polymerase sigma factor
protein_id : WP_003107976.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271792/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP032257.1 Protein Homology CDS 739 1248 . - 0 ID=cds-WP_003107976.1;Parent=gene-AM490_RS00775;Dbxref=GenBank:WP_003107976.1;Name=WP_003107976.1;Ontology_term=GO:0006352,GO:0006355,GO:0003700,GO:0016987;gbkey=CDS;go_function=DNA-binding transcription factor activity|0003700||IEA,sigma factor activity|0016987||IEA;go_process=DNA-templated transcription initiation|0006352||IEA,regulation of DNA-templated transcription|0006355||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250783.1;locus_tag=AM490_RS00775;product=sigma-70 family RNA polymerase sigma factor;protein_id=WP_003107976.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM490_RS00780' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM490_RS00780' for NZ_CP032257.1 Protein Homology CDS 1350 2543 -
dbxref : GenBank:WP_003158692.1
gbkey : CDS
go_component : plasma membrane|0005886||IEA,membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003158692.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250782.1
locus_tag : AM490_RS00780
name : WP_003158692.1
ontology_term : GO:0055085,GO:0022857,GO:0005886,GO:0016020
parent : gene-AM490_RS00780
product : MFS transporter
protein_id : WP_003158692.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271792/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP032257.1 Protein Homology CDS 1351 2544 . - 0 ID=cds-WP_003158692.1;Parent=gene-AM490_RS00780;Dbxref=GenBank:WP_003158692.1;Name=WP_003158692.1;Ontology_term=GO:0055085,GO:0022857,GO:0005886,GO:0016020;gbkey=CDS;go_component=plasma membrane|0005886||IEA,membrane|0016020||IEA;go_function=transmembrane transporter activity|0022857||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250782.1;locus_tag=AM490_RS00780 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271793/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271793/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271793/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271793/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271793/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB86_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB86_RS00005' for NZ_QMGI01000001.1 Protein Homology CDS 0 1205 -
dbxref : GenBank:WP_114012832.1
gbkey : CDS
go_function : ATP binding|0005524||IEA
go_process : protein secretion|0009306||IEA
id : cds-WP_114012832.1
inference : COORDINATES: protein motif:HMM:NF012652.5
locus_tag : CSB86_RS00005
name : WP_114012832.1
ontology_term : GO:0009306,GO:0005524
parent : gene-CSB86_RS00005
partial : true
product : GspE/PulE family protein
protein_id : WP_114012832.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271793/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_QMGI01000001.1 Protein Homology CDS 1 1206 . - 0 ID=cds-WP_114012832.1;Parent=gene-CSB86_RS00005;Dbxref=GenBank:WP_114012832.1;Name=WP_114012832.1;Ontology_term=GO:0009306,GO:0005524;gbkey=CDS;go_function=ATP binding|0005524||IEA;go_process=protein secretion|0009306||IEA;inference=COORDINATES: protein motif:HMM:NF012652.5;locus_tag=CSB86_RS00005;partial=true;product=GspE/PulE family protein;protein_id=WP_114012832.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB86_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB86_RS00010' for NZ_QMGI01000001.1 Protein Homology CDS 1225 1746 -
dbxref : GenBank:WP_023100603.1
gbkey : CDS
gene : pilP
go_process : pilus assembly|0009297||IEA
id : cds-WP_023100603.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009684378.1
locus_tag : CSB86_RS00010
name : WP_023100603.1
ontology_term : GO:0009297
parent : gene-CSB86_RS00010
product : type IV pilus biogenesis protein PilP
protein_id : WP_023100603.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271793/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_QMGI01000001.1 Protein Homology CDS 1226 1747 . - 0 ID=cds-WP_023100603.1;Parent=gene-CSB86_RS00010;Dbxref=GenBank:WP_023100603.1;Name=WP_023100603.1;Ontology_term=GO:0009297;gbkey=CDS;gene=pilP;go_process=pilus assembly|0009297||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009684378.1;locus_tag=CSB86_RS00010;product=type IV pilus biogenesis protein PilP;protein_id=WP_023100603.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB86_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB86_RS00015' for NZ_QMGI01000001.1 Protein Homology CDS 1733 3073 -
dbxref : GenBank:WP_034017950.1
gbkey : CDS
gene : pilO2
id : cds-WP_034017950.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015026534.1
locus_tag : CSB86_RS00015
name : WP_034017950.1
parent : gene-CSB86_RS00015
product : type 4b pilus protein PilO2
protein_i |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271794/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271794/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271794/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271794/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271794/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC42_RS34905' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC42_RS34905' for NZ_QMGO01000001.1 Protein Homology CDS 0 104 -
dbxref : GenBank:WP_309473543.1
gbkey : CDS
id : cds-WP_309473543.1
inference : COORDINATES: protein motif:HMM:NF017850.5
locus_tag : CSC42_RS34905
name : WP_309473543.1
parent : gene-CSC42_RS34905
partial : true
product : DUF935 family protein
protein_id : WP_309473543.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271794/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_QMGO01000001.1 Protein Homology CDS 1 105 . - 0 ID=cds-WP_309473543.1;Parent=gene-CSC42_RS34905;Dbxref=GenBank:WP_309473543.1;Name=WP_309473543.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF017850.5;locus_tag=CSC42_RS34905;partial=true;product=DUF935 family protein;protein_id=WP_309473543.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC42_RS34915' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC42_RS34915' for NZ_QMGO01000001.1 GeneMarkS-2+ CDS 337 456 -
dbxref : GenBank:WP_258550052.1
gbkey : CDS
id : cds-WP_258550052.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC42_RS34915
name : WP_258550052.1
parent : gene-CSC42_RS34915
product : DUF935 domain-containing protein
protein_id : WP_258550052.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271794/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_QMGO01000001.1 GeneMarkS-2+ CDS 338 457 . - 0 ID=cds-WP_258550052.1;Parent=gene-CSC42_RS34915;Dbxref=GenBank:WP_258550052.1;Name=WP_258550052.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC42_RS34915;product=DUF935 domain-containing protein;protein_id=WP_258550052.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC42_RS34920' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC42_RS34920' for NZ_QMGO01000001.1 Protein Homology CDS 553 696 -
dbxref : GenBank:WP_258550053.1
gbkey : CDS
id : cds-WP_258550053.1
inference : COORDINATES: protein motif:HMM:TIGR01630.1
locus_tag : CSC42_RS34920
name : WP_258550053.1
parent : gene-CSC42_RS34920
product : hypothetical protein
protein_id : WP_258550053.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271794/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_QMGO01000001.1 Protein Homology CDS 554 697 . - 0 ID=cds-WP_258550053.1;Parent=gene-CSC42_RS34920;Dbxref=GenBank:WP_258550053.1;Name=WP_258550053.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:TIGR01630.1;locus_tag=CSC42_RS34920;product=hypothetical protein;protein_id=WP_258550053.1;transl_table=11'
WARNING_TRA |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271795/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271795/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271795/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271795/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271795/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB89_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB89_RS00010' for NZ_QMGJ01000001.1 GeneMarkS-2+ CDS 1346 1765 +
dbxref : GenBank:WP_114012134.1
gbkey : CDS
id : cds-WP_114012134.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSB89_RS00010
name : WP_114012134.1
parent : gene-CSB89_RS00010
product : hypothetical protein
protein_id : WP_114012134.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271795/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_QMGJ01000001.1 GeneMarkS-2+ CDS 1347 1766 . + 0 ID=cds-WP_114012134.1;Parent=gene-CSB89_RS00010;Dbxref=GenBank:WP_114012134.1;Name=WP_114012134.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSB89_RS00010;product=hypothetical protein;protein_id=WP_114012134.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB89_RS30615' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB89_RS30615' for NZ_QMGJ01000001.1 Protein Homology CDS 1802 3436 +
dbxref : GenBank:WP_258550203.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : transporter activity|0005215||IEA
go_process : transport|0006810||IEA
id : cds-WP_258550203.1
inference : COORDINATES: protein motif:HMM:NF013069.5
locus_tag : CSB89_RS30615
name : WP_258550203.1
ontology_term : GO:0006810,GO:0005215,GO:0016020
parent : gene-CSB89_RS30615
product : efflux RND transporter periplasmic adaptor subunit
protein_id : WP_258550203.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271795/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_QMGJ01000001.1 Protein Homology CDS 1803 3437 . + 0 ID=cds-WP_258550203.1;Parent=gene-CSB89_RS30615;Dbxref=GenBank:WP_258550203.1;Name=WP_258550203.1;Ontology_term=GO:0006810,GO:0005215,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=transporter activity|0005215||IEA;go_process=transport|0006810||IEA;inference=COORDINATES: protein motif:HMM:NF013069.5;locus_tag=CSB89_RS30615;product=efflux RND transporter periplasmic adaptor subunit;protein_id=WP_258550203.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB89_RS30620' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB89_RS30620' for NZ_QMGJ01000001.1 Protein Homology CDS 3433 5166 +
dbxref : GenBank:WP_258550204.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_258550204.1
inference : COORDINATES: protein motif:HMM:NF013069.5
locus_tag : CSB89_RS30620
name : WP_258550204.1
ontology_term : GO:0055085,GO:0022857,GO:0016020
parent : gene-CSB89_RS30620
product : efflux RND tra |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271796/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271796/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271796/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271796/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271796/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC36_RS33255' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC36_RS33255' for NZ_QMGL01000001.1 Protein Homology CDS 525 941 +
dbxref : GenBank:WP_181854201.1
gbkey : CDS
id : cds-WP_181854201.1
inference : COORDINATES: protein motif:HMM:NF040129.2
locus_tag : CSC36_RS33255
name : WP_181854201.1
parent : gene-CSC36_RS33255
product : tape measure protein
protein_id : WP_181854201.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271796/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_QMGL01000001.1 Protein Homology CDS 526 942 . + 0 ID=cds-WP_181854201.1;Parent=gene-CSC36_RS33255;Dbxref=GenBank:WP_181854201.1;Name=WP_181854201.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF040129.2;locus_tag=CSC36_RS33255;product=tape measure protein;protein_id=WP_181854201.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC36_RS33260' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC36_RS33260' for NZ_QMGL01000001.1 GeneMarkS-2+ CDS 1203 1601 +
dbxref : GenBank:WP_181854203.1
gbkey : CDS
id : cds-WP_181854203.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC36_RS33260
name : WP_181854203.1
parent : gene-CSC36_RS33260
product : hypothetical protein
protein_id : WP_181854203.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271796/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_QMGL01000001.1 GeneMarkS-2+ CDS 1204 1602 . + 0 ID=cds-WP_181854203.1;Parent=gene-CSC36_RS33260;Dbxref=GenBank:WP_181854203.1;Name=WP_181854203.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC36_RS33260;product=hypothetical protein;protein_id=WP_181854203.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC36_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC36_RS00010' for NZ_QMGL01000001.1 GeneMarkS-2+ CDS 2180 2569 +
dbxref : GenBank:WP_181854204.1
gbkey : CDS
id : cds-WP_181854204.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC36_RS00010
name : WP_181854204.1
parent : gene-CSC36_RS00010
product : hypothetical protein
protein_id : WP_181854204.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271796/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_QMGL01000001.1 GeneMarkS-2+ CDS 2181 2570 . + 0 ID=cds-WP_181854204.1;Parent=gene-CSC36_RS00010;Dbxref=GenBank:WP_181854204.1;Name=WP_181854204.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC36_RS00010;product=hypothetical protein;protein_id=WP_181854204.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC36_RS33715' is a Gene instead of a tr |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271797/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271797/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271797/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271797/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271797/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC43_RS36380' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC43_RS36380' for NZ_QMGP01000001.1 GeneMarkS-2+ CDS 839 1084 -
dbxref : GenBank:WP_258552229.1
gbkey : CDS
id : cds-WP_258552229.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC43_RS36380
name : WP_258552229.1
parent : gene-CSC43_RS36380
product : hypothetical protein
protein_id : WP_258552229.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271797/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_QMGP01000001.1 GeneMarkS-2+ CDS 840 1085 . - 0 ID=cds-WP_258552229.1;Parent=gene-CSC43_RS36380;Dbxref=GenBank:WP_258552229.1;Name=WP_258552229.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC43_RS36380;product=hypothetical protein;protein_id=WP_258552229.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC43_RS36845' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC43_RS36845' for NZ_QMGP01000001.1 GeneMarkS-2+ CDS 1724 2059 +
dbxref : GenBank:WP_404936647.1
gbkey : CDS
id : cds-WP_404936647.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC43_RS36845
name : WP_404936647.1
parent : gene-CSC43_RS36845
product : hypothetical protein
protein_id : WP_404936647.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271797/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_QMGP01000001.1 GeneMarkS-2+ CDS 1725 2060 . + 0 ID=cds-WP_404936647.1;Parent=gene-CSC43_RS36845;Dbxref=GenBank:WP_404936647.1;Name=WP_404936647.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC43_RS36845;product=hypothetical protein;protein_id=WP_404936647.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC43_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC43_RS00015' for NZ_QMGP01000001.1 Protein Homology CDS 2010 2468 -
dbxref : GenBank:WP_220186539.1
gbkey : CDS
id : cds-WP_220186539.1
inference : COORDINATES: protein motif:HMM:NF015431.5
locus_tag : CSC43_RS00015
name : WP_220186539.1
parent : gene-CSC43_RS00015
product : LysR substrate-binding domain-containing protein
protein_id : WP_220186539.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271797/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_QMGP01000001.1 Protein Homology CDS 2011 2469 . - 0 ID=cds-WP_220186539.1;Parent=gene-CSC43_RS00015;Dbxref=GenBank:WP_220186539.1;Name=WP_220186539.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF015431.5;locus_tag=CSC43_RS00015;product=LysR substrate-binding domain-containing protein;protein_id=WP_220186539.1;transl_table=11'
WARNING_GENE_NOT_FOUND: Gene 'null' ( |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271798/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271798/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271798/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271798/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271798/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC45_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC45_RS00015' for NZ_QMGQ01000001.1 Protein Homology CDS 700 1149 -
dbxref : GenBank:WP_015649664.1
gbkey : CDS
id : cds-WP_015649664.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012613778.1
locus_tag : CSC45_RS00015
name : WP_015649664.1
parent : gene-CSC45_RS00015
product : Mor transcription activator family protein
protein_id : WP_015649664.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271798/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_QMGQ01000001.1 Protein Homology CDS 701 1150 . - 0 ID=cds-WP_015649664.1;Parent=gene-CSC45_RS00015;Dbxref=GenBank:WP_015649664.1;Name=WP_015649664.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012613778.1;locus_tag=CSC45_RS00015;product=Mor transcription activator family protein;protein_id=WP_015649664.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC45_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC45_RS00020' for NZ_QMGQ01000001.1 Protein Homology CDS 1136 1543 -
dbxref : GenBank:WP_015972859.1
gbkey : CDS
id : cds-WP_015972859.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003099430.1
locus_tag : CSC45_RS00020
name : WP_015972859.1
parent : gene-CSC45_RS00020
product : gp16 family protein
protein_id : WP_015972859.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271798/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_QMGQ01000001.1 Protein Homology CDS 1137 1544 . - 0 ID=cds-WP_015972859.1;Parent=gene-CSC45_RS00020;Dbxref=GenBank:WP_015972859.1;Name=WP_015972859.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003099430.1;locus_tag=CSC45_RS00020;product=gp16 family protein;protein_id=WP_015972859.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC45_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC45_RS00025' for NZ_QMGQ01000001.1 Protein Homology CDS 1540 1836 -
dbxref : GenBank:WP_003099427.1
gbkey : CDS
id : cds-WP_003099427.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_016068559.1
locus_tag : CSC45_RS00025
name : WP_003099427.1
parent : gene-CSC45_RS00025
product : hypothetical protein
protein_id : WP_003099427.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271798/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_QMGQ01000001.1 Protein Homology CDS 1541 1837 . - 0 ID=cds-WP_003099427.1;Parent=gene-CSC45_RS00025;Dbxref=GenBank:WP_003099427.1;Name=WP_003099427.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016068559.1;locus_tag=CSC45_RS00025;product=h |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271799/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271799/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271799/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271799/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271799/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC46_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC46_RS00005' for NZ_CP030351.1 Protein Homology CDS 6 458 +
dbxref : GenBank:WP_003102319.1
gbkey : CDS
go_function : FMN binding|0010181||IEA
id : cds-WP_003102319.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252125.1
locus_tag : CSC46_RS00005
name : WP_003102319.1
ontology_term : GO:0010181
parent : gene-CSC46_RS00005
product : flavodoxin
protein_id : WP_003102319.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271799/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP030351.1 Protein Homology CDS 7 459 . + 0 ID=cds-WP_003102319.1;Parent=gene-CSC46_RS00005;Dbxref=GenBank:WP_003102319.1;Name=WP_003102319.1;Ontology_term=GO:0010181;gbkey=CDS;go_function=FMN binding|0010181||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252125.1;locus_tag=CSC46_RS00005;product=flavodoxin;protein_id=WP_003102319.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC46_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC46_RS00010' for NZ_CP030351.1 Protein Homology CDS 698 1591 -
dbxref : GenBank:WP_003091888.1
gbkey : CDS
id : cds-WP_003091888.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252123.1
locus_tag : CSC46_RS00010
name : WP_003091888.1
parent : gene-CSC46_RS00010
product : LysR family transcriptional regulator
protein_id : WP_003091888.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271799/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP030351.1 Protein Homology CDS 699 1592 . - 0 ID=cds-WP_003091888.1;Parent=gene-CSC46_RS00010;Dbxref=GenBank:WP_003091888.1;Name=WP_003091888.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252123.1;locus_tag=CSC46_RS00010;product=LysR family transcriptional regulator;protein_id=WP_003091888.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC46_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC46_RS00015' for NZ_CP030351.1 Protein Homology CDS 1687 2076 +
dbxref : GenBank:WP_003091885.1
gbkey : CDS
go_component : membrane|0016020||IEA
id : cds-WP_003091885.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252122.1
locus_tag : CSC46_RS00015
name : WP_003091885.1
ontology_term : GO:0016020
parent : gene-CSC46_RS00015
product : CidA/LrgA family protein
protein_id : WP_003091885.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271799/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_CP030351.1 Protein Homology CDS 1688 2077 . + 0 ID=cds-WP_003091885.1;Parent=gene-CSC46_RS00015;Dbxref=GenBank:WP_003091885.1;Name= |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271800/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271800/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271800/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271800/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271800/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM489_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM489_RS00010' for NZ_CP029745.1 Protein Homology CDS 443 2680 -
dbxref : GenBank:WP_031638514.1
gbkey : CDS
id : cds-WP_031638514.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249316.1
locus_tag : AM489_RS00010
name : WP_031638514.1
parent : gene-AM489_RS00010
product : phage tail length tape measure protein
protein_id : WP_031638514.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271800/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP029745.1 Protein Homology CDS 444 2681 . - 0 ID=cds-WP_031638514.1;Parent=gene-AM489_RS00010;Dbxref=GenBank:WP_031638514.1;Name=WP_031638514.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249316.1;locus_tag=AM489_RS00010;product=phage tail length tape measure protein;protein_id=WP_031638514.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM489_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM489_RS00015' for NZ_CP029745.1 Protein Homology CDS 2850 3194 -
dbxref : GenBank:WP_003085178.1
gbkey : CDS
go_process : viral tail assembly|0098003||IEA
id : cds-WP_003085178.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249315.1
locus_tag : AM489_RS00015
name : WP_003085178.1
ontology_term : GO:0098003
parent : gene-AM489_RS00015
product : phage tail assembly protein
protein_id : WP_003085178.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271800/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029745.1 Protein Homology CDS 2851 3195 . - 0 ID=cds-WP_003085178.1;Parent=gene-AM489_RS00015;Dbxref=GenBank:WP_003085178.1;Name=WP_003085178.1;Ontology_term=GO:0098003;gbkey=CDS;go_process=viral tail assembly|0098003||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249315.1;locus_tag=AM489_RS00015;product=phage tail assembly protein;protein_id=WP_003085178.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM489_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM489_RS00020' for NZ_CP029745.1 Protein Homology CDS 3209 3712 -
dbxref : GenBank:WP_003085175.1
gbkey : CDS
go_component : virion component|0044423||IEA
go_function : structural molecule activity|0005198||IEA
go_process : viral process|0016032||IEA
id : cds-WP_003085175.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249314.1
locus_tag : AM489_RS00020
name : WP_003085175.1
ontology_term : GO:0016032,GO:0005198,GO:0044423
parent : gene-AM489_RS00020
product : phage major tail tube protein
protein_id : WP_003085175.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jo |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271801/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271801/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271801/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271801/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271801/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CLH63_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CLH63_RS00020' for NZ_CP023255.1 Protein Homology CDS 675 1712 -
dbxref : GenBank:WP_003116451.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA
go_process : regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003116451.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251784.1
locus_tag : CLH63_RS00020
name : WP_003116451.1
ontology_term : GO:0006355,GO:0003677,GO:0003700
parent : gene-CLH63_RS00020
product : AraC family transcriptional regulator
protein_id : WP_003116451.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271801/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 21 'NZ_CP023255.1 Protein Homology CDS 676 1713 . - 0 ID=cds-WP_003116451.1;Parent=gene-CLH63_RS00020;Dbxref=GenBank:WP_003116451.1;Name=WP_003116451.1;Ontology_term=GO:0006355,GO:0003677,GO:0003700;gbkey=CDS;go_function=DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA;go_process=regulation of DNA-templated transcription|0006355||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251784.1;locus_tag=CLH63_RS00020;product=AraC family transcriptional regulator;protein_id=WP_003116451.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CLH63_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CLH63_RS00025' for NZ_CP023255.1 Protein Homology CDS 1709 2827 -
dbxref : GenBank:WP_003113936.1
gbkey : CDS
go_process : metabolic process|0008152||IEA
id : cds-WP_003113936.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251783.1
locus_tag : CLH63_RS00025
name : WP_003113936.1
ontology_term : GO:0008152
parent : gene-CLH63_RS00025
product : carbon-nitrogen hydrolase family protein
protein_id : WP_003113936.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271801/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 23 'NZ_CP023255.1 Protein Homology CDS 1710 2828 . - 0 ID=cds-WP_003113936.1;Parent=gene-CLH63_RS00025;Dbxref=GenBank:WP_003113936.1;Name=WP_003113936.1;Ontology_term=GO:0008152;gbkey=CDS;go_process=metabolic process|0008152||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251783.1;locus_tag=CLH63_RS00025;product=carbon-nitrogen hydrolase family protein;protein_id=WP_003113936.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CLH63_RS00030' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CLH63_RS00030' for NZ_CP023255.1 Protein Homology CDS 3042 5081 +
dbxref : GenBank:WP_023088184.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA
id : cds-WP_023088184.1
inference : COORDINATES: similar |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271802/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271802/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271802/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271802/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271802/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC33_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC33_RS00005' for NZ_CP029660.1 Protein Homology CDS 96 1073 -
dbxref : GenBank:WP_031638751.1
gbkey : CDS
go_function : DNA binding|0003677||IEA
go_process : phosphorelay signal transduction system|0000160||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_031638751.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252460.1
locus_tag : CSC33_RS00005
name : WP_031638751.1
ontology_term : GO:0000160,GO:0006355,GO:0003677
parent : gene-CSC33_RS00005
product : helix-turn-helix transcriptional regulator
protein_id : WP_031638751.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271802/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP029660.1 Protein Homology CDS 97 1074 . - 0 ID=cds-WP_031638751.1;Parent=gene-CSC33_RS00005;Dbxref=GenBank:WP_031638751.1;Name=WP_031638751.1;Ontology_term=GO:0000160,GO:0006355,GO:0003677;gbkey=CDS;go_function=DNA binding|0003677||IEA;go_process=phosphorelay signal transduction system|0000160||IEA,regulation of DNA-templated transcription|0006355||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252460.1;locus_tag=CSC33_RS00005;product=helix-turn-helix transcriptional regulator;protein_id=WP_031638751.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC33_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC33_RS00010' for NZ_CP029660.1 Protein Homology CDS 1337 2806 +
dbxref : GenBank:WP_003092702.1
gbkey : CDS
gene : guaB
go_function : IMP dehydrogenase activity|0003938||IEA
go_process : purine nucleotide biosynthetic process|0006164||IEA
id : cds-WP_003092702.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252459.1
locus_tag : CSC33_RS00010
name : WP_003092702.1
ontology_term : GO:0006164,GO:0003938
parent : gene-CSC33_RS00010
product : IMP dehydrogenase
protein_id : WP_003092702.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271802/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029660.1 Protein Homology CDS 1338 2807 . + 0 ID=cds-WP_003092702.1;Parent=gene-CSC33_RS00010;Dbxref=GenBank:WP_003092702.1;Name=WP_003092702.1;Ontology_term=GO:0006164,GO:0003938;gbkey=CDS;gene=guaB;go_function=IMP dehydrogenase activity|0003938||IEA;go_process=purine nucleotide biosynthetic process|0006164||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252459.1;locus_tag=CSC33_RS00010;product=IMP dehydrogenase;protein_id=WP_003092702.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC33_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC33_RS00015' for NZ_CP029660.1 Protein Homology CDS 2886 4463 +
dbxref : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271803/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271803/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271803/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271803/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271803/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC31_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC31_RS00005' for NZ_CP029089.1 Protein Homology CDS 9 395 -
dbxref : GenBank:WP_003094405.1
gbkey : CDS
go_function : peroxiredoxin activity|0051920||IEA
id : cds-WP_003094405.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253176.1
locus_tag : CSC31_RS00005
name : WP_003094405.1
ontology_term : GO:0051920
parent : gene-CSC31_RS00005
product : carboxymuconolactone decarboxylase family protein
protein_id : WP_003094405.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271803/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP029089.1 Protein Homology CDS 10 396 . - 0 ID=cds-WP_003094405.1;Parent=gene-CSC31_RS00005;Dbxref=GenBank:WP_003094405.1;Name=WP_003094405.1;Ontology_term=GO:0051920;gbkey=CDS;go_function=peroxiredoxin activity|0051920||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253176.1;locus_tag=CSC31_RS00005;product=carboxymuconolactone decarboxylase family protein;protein_id=WP_003094405.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC31_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC31_RS00010' for NZ_CP029089.1 Protein Homology CDS 427 804 -
dbxref : GenBank:WP_003116225.1
gbkey : CDS
go_function : lytic endotransglycosylase activity|0008932||IEA
go_process : cell wall organization|0071555||IEA
id : cds-WP_003116225.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253175.1
locus_tag : CSC31_RS00010
name : WP_003116225.1
ontology_term : GO:0071555,GO:0008932
parent : gene-CSC31_RS00010
product : septal ring lytic transglycosylase RlpA family protein
protein_id : WP_003116225.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271803/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029089.1 Protein Homology CDS 428 805 . - 0 ID=cds-WP_003116225.1;Parent=gene-CSC31_RS00010;Dbxref=GenBank:WP_003116225.1;Name=WP_003116225.1;Ontology_term=GO:0071555,GO:0008932;gbkey=CDS;go_function=lytic endotransglycosylase activity|0008932||IEA;go_process=cell wall organization|0071555||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253175.1;locus_tag=CSC31_RS00010;product=septal ring lytic transglycosylase RlpA family protein;protein_id=WP_003116225.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC31_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC31_RS00015' for NZ_CP029089.1 Protein Homology CDS 864 2324 -
dbxref : GenBank:WP_071536084.1
gbkey : CDS
gene : gatB
go_function : carbon-nitrogen ligase activity%2C with glutamine as amido-N-donor|0016884||IEA
id : cds-WP_071536084.1
inference : COORDINATES: similar to |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271804/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271804/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271804/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271804/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271804/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC32_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC32_RS00005' for NZ_CP029088.1 Protein Homology CDS 0 1544 +
dbxref : GenBank:WP_003109151.1
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003109151.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064721.1
locus_tag : CSC32_RS00005
name : WP_003109151.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-CSC32_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003109151.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271804/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP029088.1 Protein Homology CDS 1 1545 . + 0 ID=cds-WP_003109151.1;Parent=gene-CSC32_RS00005;Dbxref=GenBank:WP_003109151.1;Name=WP_003109151.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_064721.1;locus_tag=CSC32_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003109151.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC32_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC32_RS00010' for NZ_CP029088.1 Protein Homology CDS 1573 2676 +
dbxref : GenBank:WP_003097262.1
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_003097262.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064722.1
locus_tag : CSC32_RS00010
name : WP_003097262.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-CSC32_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_003097262.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271804/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029088.1 Protein Homology CDS 1574 2677 . + 0 ID=cds-WP_003097262.1;Parent=gene-CSC32_RS00010;Dbxref=GenBank:WP_003097262.1;Name=WP_003097262.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDIN |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271805/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271805/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271805/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271805/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271805/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC26_RS02590' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC26_RS02590' for NZ_CP029097.1 Protein Homology CDS 641 1540 -
dbxref : GenBank:WP_003158509.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA,metal ion binding|0046872||IEA
id : cds-WP_003158509.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248884.1
locus_tag : CSC26_RS02590
name : WP_003158509.1
ontology_term : GO:0016491,GO:0046872
parent : gene-CSC26_RS02590
product : TauD/TfdA dioxygenase family protein
protein_id : WP_003158509.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271805/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP029097.1 Protein Homology CDS 642 1541 . - 0 ID=cds-WP_003158509.1;Parent=gene-CSC26_RS02590;Dbxref=GenBank:WP_003158509.1;Name=WP_003158509.1;Ontology_term=GO:0016491,GO:0046872;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA,metal ion binding|0046872||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248884.1;locus_tag=CSC26_RS02590;product=TauD/TfdA dioxygenase family protein;protein_id=WP_003158509.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC26_RS02595' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC26_RS02595' for NZ_CP029097.1 Protein Homology CDS 1608 2510 -
dbxref : GenBank:WP_003118597.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA,metal ion binding|0046872||IEA
id : cds-WP_003118597.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248883.1
locus_tag : CSC26_RS02595
name : WP_003118597.1
ontology_term : GO:0016491,GO:0046872
parent : gene-CSC26_RS02595
product : TauD/TfdA dioxygenase family protein
protein_id : WP_003118597.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271805/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029097.1 Protein Homology CDS 1609 2511 . - 0 ID=cds-WP_003118597.1;Parent=gene-CSC26_RS02595;Dbxref=GenBank:WP_003118597.1;Name=WP_003118597.1;Ontology_term=GO:0016491,GO:0046872;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA,metal ion binding|0046872||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248883.1;locus_tag=CSC26_RS02595;product=TauD/TfdA dioxygenase family protein;protein_id=WP_003118597.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC26_RS02600' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC26_RS02600' for NZ_CP029097.1 Protein Homology CDS 2551 4923 -
dbxref : GenBank:WP_023083666.1
gbkey : CDS
go_component : cell outer membrane|0009279||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_023083666.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248882.1
locus_tag |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271806/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271806/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271806/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271806/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271806/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC27_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC27_RS00005' for NZ_CP029148.1 GeneMarkS-2+ CDS 0 214 -
dbxref : GenBank:WP_108703099.1
gbkey : CDS
id : cds-WP_108703099.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC27_RS00005
name : WP_108703099.1
parent : gene-CSC27_RS00005
partial : true
product : hypothetical protein
protein_id : WP_108703099.1
source : GeneMarkS-2+
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271806/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP029148.1 GeneMarkS-2+ CDS 1 215 . - 0 ID=cds-WP_108703099.1;Parent=gene-CSC27_RS00005;Dbxref=GenBank:WP_108703099.1;Name=WP_108703099.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC27_RS00005;partial=true;product=hypothetical protein;protein_id=WP_108703099.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC27_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC27_RS00025' for NZ_CP029148.1 Protein Homology CDS 1227 1898 -
dbxref : GenBank:WP_239066672.1
gbkey : CDS
id : cds-WP_239066672.1
inference : COORDINATES: protein motif:HMM:NF013618.6
locus_tag : CSC27_RS00025
name : WP_239066672.1
parent : gene-CSC27_RS00025
product : transglycosylase SLT domain-containing protein
protein_id : WP_239066672.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271806/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_CP029148.1 Protein Homology CDS 1228 1899 . - 0 ID=cds-WP_239066672.1;Parent=gene-CSC27_RS00025;Dbxref=GenBank:WP_239066672.1;Name=WP_239066672.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF013618.6;locus_tag=CSC27_RS00025;product=transglycosylase SLT domain-containing protein;protein_id=WP_239066672.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC27_RS35320' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC27_RS35320' for NZ_CP029148.1 GeneMarkS-2+ CDS 2002 2160 -
dbxref : GenBank:WP_162832300.1
gbkey : CDS
id : cds-WP_162832300.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC27_RS35320
name : WP_162832300.1
parent : gene-CSC27_RS35320
product : hypothetical protein
protein_id : WP_162832300.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271806/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_CP029148.1 GeneMarkS-2+ CDS 2003 2161 . - 0 ID=cds-WP_162832300.1;Parent=gene-CSC27_RS35320;Dbxref=GenBank:WP_162832300.1;Name=WP_162832300.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC27_RS35320;product=hypothetical protein;protein_id=WP_162832300.1;transl_table=11'
WARNIN |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271807/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271807/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271807/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271807/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271807/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC30_RS32575' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC30_RS32575' for NZ_CP029147.1 GeneMarkS-2+ CDS 368 523 +
dbxref : GenBank:WP_239066652.1
gbkey : CDS
id : cds-WP_239066652.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC30_RS32575
name : WP_239066652.1
parent : gene-CSC30_RS32575
product : hypothetical protein
protein_id : WP_239066652.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271807/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029147.1 GeneMarkS-2+ CDS 369 524 . + 0 ID=cds-WP_239066652.1;Parent=gene-CSC30_RS32575;Dbxref=GenBank:WP_239066652.1;Name=WP_239066652.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC30_RS32575;product=hypothetical protein;protein_id=WP_239066652.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC30_RS32580' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC30_RS32580' for NZ_CP029147.1 Protein Homology CDS 520 996 +
dbxref : GenBank:WP_239066653.1
gbkey : CDS
id : cds-WP_239066653.1
inference : COORDINATES: protein motif:HMM:NF017518.6
locus_tag : CSC30_RS32580
name : WP_239066653.1
parent : gene-CSC30_RS32580
product : zonular occludens toxin domain-containing protein
protein_id : WP_239066653.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271807/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_CP029147.1 Protein Homology CDS 521 997 . + 0 ID=cds-WP_239066653.1;Parent=gene-CSC30_RS32580;Dbxref=GenBank:WP_239066653.1;Name=WP_239066653.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF017518.6;locus_tag=CSC30_RS32580;product=zonular occludens toxin domain-containing protein;protein_id=WP_239066653.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC30_RS32585' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC30_RS32585' for NZ_CP029147.1 GeneMarkS-2+ CDS 1055 1408 +
dbxref : GenBank:WP_239066654.1
gbkey : CDS
id : cds-WP_239066654.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC30_RS32585
name : WP_239066654.1
parent : gene-CSC30_RS32585
product : hypothetical protein
protein_id : WP_239066654.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271807/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_CP029147.1 GeneMarkS-2+ CDS 1056 1409 . + 0 ID=cds-WP_239066654.1;Parent=gene-CSC30_RS32585;Dbxref=GenBank:WP_239066654.1;Name=WP_239066654.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC30_RS32585;product=hypothetical protein;protein_id=WP_239066654.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC30_RS00015 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271808/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271808/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271808/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271808/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271808/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB88_RS31535' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB88_RS31535' for NZ_PSQP01000001.1 GeneMarkS-2+ CDS 636 1532 -
dbxref : GenBank:WP_181186658.1
gbkey : CDS
id : cds-WP_181186658.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSB88_RS31535
name : WP_181186658.1
parent : gene-CSB88_RS31535
product : hypothetical protein
protein_id : WP_181186658.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271808/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_PSQP01000001.1 GeneMarkS-2+ CDS 637 1533 . - 0 ID=cds-WP_181186658.1;Parent=gene-CSB88_RS31535;Dbxref=GenBank:WP_181186658.1;Name=WP_181186658.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSB88_RS31535;product=hypothetical protein;protein_id=WP_181186658.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB88_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB88_RS00010' for NZ_PSQP01000001.1 Protein Homology CDS 1592 4321 -
dbxref : GenBank:WP_106120476.1
gbkey : CDS
id : cds-WP_106120476.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012614035.1
locus_tag : CSB88_RS00010
name : WP_106120476.1
parent : gene-CSB88_RS00010
product : host specificity factor TipJ family phage tail protein
protein_id : WP_106120476.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271808/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_PSQP01000001.1 Protein Homology CDS 1593 4322 . - 0 ID=cds-WP_106120476.1;Parent=gene-CSB88_RS00010;Dbxref=GenBank:WP_106120476.1;Name=WP_106120476.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012614035.1;locus_tag=CSB88_RS00010;product=host specificity factor TipJ family phage tail protein;protein_id=WP_106120476.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB88_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB88_RS00015' for NZ_PSQP01000001.1 Protein Homology CDS 4293 4700 -
dbxref : GenBank:WP_023082970.1
gbkey : CDS
id : cds-WP_023082970.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003131216.1
locus_tag : CSB88_RS00015
name : WP_023082970.1
parent : gene-CSB88_RS00015
product : C40 family peptidase
protein_id : WP_023082970.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271808/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_PSQP01000001.1 Protein Homology CDS 4294 4701 . - 0 ID=cds-WP_023082970.1;Parent=gene-CSB88_RS00015;Dbxref=GenBank:WP_023082970.1;Name=WP_023082970.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003131216.1;locus_tag=CSB88_RS00015;product=C40 fami |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271809/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271809/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271809/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271809/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271809/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB96_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB96_RS00005' for NZ_PSQS01000001.1 Protein Homology CDS 523 981 -
dbxref : GenBank:WP_044596211.1
gbkey : CDS
gene : traD
id : cds-WP_044596211.1
inference : COORDINATES: protein motif:HMM:NF018152.6
locus_tag : CSB96_RS00005
name : WP_044596211.1
parent : gene-CSB96_RS00005
product : conjugal transfer protein TraD
protein_id : WP_044596211.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271809/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_PSQS01000001.1 Protein Homology CDS 524 982 . - 0 ID=cds-WP_044596211.1;Parent=gene-CSB96_RS00005;Dbxref=GenBank:WP_044596211.1;Name=WP_044596211.1;gbkey=CDS;gene=traD;inference=COORDINATES: protein motif:HMM:NF018152.6;locus_tag=CSB96_RS00005;product=conjugal transfer protein TraD;protein_id=WP_044596211.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB96_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB96_RS00010' for NZ_PSQS01000001.1 Protein Homology CDS 1156 2592 +
dbxref : GenBank:WP_106120737.1
gbkey : CDS
id : cds-WP_106120737.1
inference : COORDINATES: protein motif:HMM:NF015354.6
locus_tag : CSB96_RS00010
name : WP_106120737.1
parent : gene-CSB96_RS00010
product : MobA/MobL family protein
protein_id : WP_106120737.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271809/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_PSQS01000001.1 Protein Homology CDS 1157 2593 . + 0 ID=cds-WP_106120737.1;Parent=gene-CSB96_RS00010;Dbxref=GenBank:WP_106120737.1;Name=WP_106120737.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF015354.6;locus_tag=CSB96_RS00010;product=MobA/MobL family protein;protein_id=WP_106120737.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB96_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB96_RS00015' for NZ_PSQS01000001.1 Protein Homology CDS 2620 3451 -
dbxref : GenBank:WP_146141583.1
end_range : 3452,.
gbkey : CDS
id : cds-WP_146141583.1
inference : COORDINATES: protein motif:HMM:NF024108.6
locus_tag : CSB96_RS00015
name : WP_146141583.1
parent : gene-CSB96_RS00015
partial : true
product : TraM recognition domain-containing protein
protein_id : WP_146141583.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271809/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_PSQS01000001.1 Protein Homology CDS 2621 3452 . - 1 ID=cds-WP_146141583.1;Parent=gene-CSB96_RS00015;Dbxref=GenBank:WP_146141583.1;Name=WP_146141583.1;end_range=3452,.;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024108.6;locus_tag=CSB96_RS00015;partial=true;product=TraM re |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271810/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271810/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271810/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271810/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271810/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY960_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY960_RS00005' for NZ_RXUF01000001.1 Protein Homology CDS 294 3389 -
dbxref : GenBank:WP_108202040.1
gbkey : CDS
gene : dnaE2
id : cds-WP_108202040.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY960_RS00005
name : WP_108202040.1
parent : gene-DY960_RS00005
product : error-prone DNA polymerase
protein_id : WP_108202040.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271810/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUF01000001.1 Protein Homology CDS 295 3390 . - 0 ID=cds-WP_108202040.1;Parent=gene-DY960_RS00005;Dbxref=GenBank:WP_108202040.1;Name=WP_108202040.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY960_RS00005;product=error-prone DNA polymerase;protein_id=WP_108202040.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY960_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY960_RS00010' for NZ_RXUF01000001.1 Protein Homology CDS 3365 4780 -
dbxref : GenBank:WP_126442754.1
gbkey : CDS
id : cds-WP_126442754.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY960_RS00010
name : WP_126442754.1
parent : gene-DY960_RS00010
product : Y-family DNA polymerase
protein_id : WP_126442754.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271810/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUF01000001.1 Protein Homology CDS 3366 4781 . - 0 ID=cds-WP_126442754.1;Parent=gene-DY960_RS00010;Dbxref=GenBank:WP_126442754.1;Name=WP_126442754.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY960_RS00010;product=Y-family DNA polymerase;protein_id=WP_126442754.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY960_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY960_RS00015' for NZ_RXUF01000001.1 Protein Homology CDS 4788 5393 -
dbxref : GenBank:WP_031627677.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031627677.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003296675.1
locus_tag : DY960_RS00015
name : WP_031627677.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY960_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031627677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271810/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUF01000001.1 Protein Homology CDS 4789 5394 . - 0 ID=cds-WP_031627677.1;Parent=gene-DY960_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271811/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271811/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271811/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271811/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271811/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY987_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY987_RS00005' for NZ_RXVI01000001.1 GeneMarkS-2+ CDS 0 1548 +
dbxref : GenBank:WP_221768621.1
gbkey : CDS
id : cds-WP_221768621.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY987_RS00005
name : WP_221768621.1
parent : gene-DY987_RS00005
partial : true
product : hypothetical protein
protein_id : WP_221768621.1
source : GeneMarkS-2+
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271811/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVI01000001.1 GeneMarkS-2+ CDS 1 1549 . + 1 ID=cds-WP_221768621.1;Parent=gene-DY987_RS00005;Dbxref=GenBank:WP_221768621.1;Name=WP_221768621.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY987_RS00005;partial=true;product=hypothetical protein;protein_id=WP_221768621.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY987_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY987_RS00010' for NZ_RXVI01000001.1 GeneMarkS-2+ CDS 1548 2555 +
dbxref : GenBank:WP_033976488.1
gbkey : CDS
id : cds-WP_033976488.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY987_RS00010
name : WP_033976488.1
parent : gene-DY987_RS00010
product : hypothetical protein
protein_id : WP_033976488.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271811/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVI01000001.1 GeneMarkS-2+ CDS 1549 2556 . + 0 ID=cds-WP_033976488.1;Parent=gene-DY987_RS00010;Dbxref=GenBank:WP_033976488.1;Name=WP_033976488.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY987_RS00010;product=hypothetical protein;protein_id=WP_033976488.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY987_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY987_RS00015' for NZ_RXVI01000001.1 Protein Homology CDS 2552 3412 +
dbxref : GenBank:WP_052188300.1
gbkey : CDS
id : cds-WP_052188300.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015648933.1
locus_tag : DY987_RS00015
name : WP_052188300.1
parent : gene-DY987_RS00015
product : hypothetical protein
protein_id : WP_052188300.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271811/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVI01000001.1 Protein Homology CDS 2553 3413 . + 0 ID=cds-WP_052188300.1;Parent=gene-DY987_RS00015;Dbxref=GenBank:WP_052188300.1;Name=WP_052188300.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015648933.1;locus_tag=DY987_RS00015;product=hypothetical protein;protein_id=WP_052188300.1;transl_table=11'
|
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271812/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271812/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271812/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271812/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271812/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY991_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY991_RS00005' for NZ_RXVM01000001.1 Protein Homology CDS 0 879 +
dbxref : GenBank:WP_126547904.1
gbkey : CDS
gene : tssI
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_126547904.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251984.1
locus_tag : DY991_RS00005
name : WP_126547904.1
ontology_term : GO:0033103
parent : gene-DY991_RS00005
partial : true
product : type VI secretion system tip protein TssI/VgrG
protein_id : WP_126547904.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271812/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVM01000001.1 Protein Homology CDS 1 880 . + 1 ID=cds-WP_126547904.1;Parent=gene-DY991_RS00005;Dbxref=GenBank:WP_126547904.1;Name=WP_126547904.1;Ontology_term=GO:0033103;gbkey=CDS;gene=tssI;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251984.1;locus_tag=DY991_RS00005;partial=true;product=type VI secretion system tip protein TssI/VgrG;protein_id=WP_126547904.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY991_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY991_RS00010' for NZ_RXVM01000001.1 Protein Homology CDS 889 1704 +
dbxref : GenBank:WP_003114071.1
gbkey : CDS
id : cds-WP_003114071.1
inference : COORDINATES: protein motif:HMM:NF024894.5
locus_tag : DY991_RS00010
name : WP_003114071.1
parent : gene-DY991_RS00010
product : DUF4123 domain-containing protein
protein_id : WP_003114071.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271812/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVM01000001.1 Protein Homology CDS 890 1705 . + 0 ID=cds-WP_003114071.1;Parent=gene-DY991_RS00010;Dbxref=GenBank:WP_003114071.1;Name=WP_003114071.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024894.5;locus_tag=DY991_RS00010;product=DUF4123 domain-containing protein;protein_id=WP_003114071.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY991_RS32205' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY991_RS32205' for NZ_RXVM01000001.1 Protein Homology CDS 2310 2558 +
dbxref : GenBank:WP_250719092.1
gbkey : CDS
id : cds-WP_250719092.1
inference : COORDINATES: protein motif:HMM:NF023173.5
locus_tag : DY991_RS32205
name : WP_250719092.1
parent : gene-DY991_RS32205
product : DUF3304 domain-containing protein
protein_id : WP_250719092.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271812/working/snpeff_output/Pseudomonasa |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271813/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271813/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271813/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271813/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271813/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY989_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY989_RS00010' for NZ_RXVK01000001.1 Protein Homology CDS 494 880 +
dbxref : GenBank:WP_071533930.1
gbkey : CDS
go_function : protein binding|0005515||IEA
id : cds-WP_071533930.1
inference : COORDINATES: protein motif:HMM:NF024206.5
locus_tag : DY989_RS00010
name : WP_071533930.1
ontology_term : GO:0005515
parent : gene-DY989_RS00010
product : ankyrin repeat domain-containing protein
protein_id : WP_071533930.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271813/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVK01000001.1 Protein Homology CDS 495 881 . + 0 ID=cds-WP_071533930.1;Parent=gene-DY989_RS00010;Dbxref=GenBank:WP_071533930.1;Name=WP_071533930.1;Ontology_term=GO:0005515;gbkey=CDS;go_function=protein binding|0005515||IEA;inference=COORDINATES: protein motif:HMM:NF024206.5;locus_tag=DY989_RS00010;product=ankyrin repeat domain-containing protein;protein_id=WP_071533930.1;transl_table=11'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_RXVK01000001.1:1-511) does not include 'gene-DY989_RS00015' (NZ_RXVK01000001.1:1070-1207). Created new gene 'null.2' (NZ_RXVK01000001.1:1070-1207). File '/jetstream2/scratch/main/jobs/72271813/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 15 'NZ_RXVK01000001.1 RefSeq pseudogene 1070 1207 . + . ID=gene-DY989_RS00015;Name=DY989_RS00015;end_range=1207,.;gbkey=Gene;gene_biotype=pseudogene;locus_tag=DY989_RS00015;old_locus_tag=DY989_00015;partial=true;pseudo=true;start_range=.,1070'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY989_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY989_RS00020' for NZ_RXVK01000001.1 GeneMarkS-2+ CDS 1580 1999 +
dbxref : GenBank:WP_124082654.1
gbkey : CDS
id : cds-WP_124082654.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY989_RS00020
name : WP_124082654.1
parent : gene-DY989_RS00020
product : hypothetical protein
protein_id : WP_124082654.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271813/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXVK01000001.1 GeneMarkS-2+ CDS 1581 2000 . + 0 ID=cds-WP_124082654.1;Parent=gene-DY989_RS00020;Dbxref=GenBank:WP_124082654.1;Name=WP_124082654.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY989_RS00020;product=hypothetical protein;protein_id=WP_124082654.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY989_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY989_RS00025' for NZ_RXVK01000001.1 GeneMarkS-2+ CDS 2603 2935 +
dbxref : GenBank:WP_023085287.1
gbkey : CDS
id : cds-WP_023085287.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
l |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271814/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271814/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271814/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271814/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271814/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA01_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA01_RS00005' for NZ_RXVW01000001.1 Protein Homology CDS 188 1207 -
dbxref : GenBank:WP_003103552.1
gbkey : CDS
gene : mexS
id : cds-WP_003103552.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251181.1
locus_tag : DZA01_RS00005
name : WP_003103552.1
parent : gene-DZA01_RS00005
product : oxidoreductase MexS
protein_id : WP_003103552.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271814/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVW01000001.1 Protein Homology CDS 189 1208 . - 0 ID=cds-WP_003103552.1;Parent=gene-DZA01_RS00005;Dbxref=GenBank:WP_003103552.1;Name=WP_003103552.1;gbkey=CDS;gene=mexS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251181.1;locus_tag=DZA01_RS00005;product=oxidoreductase MexS;protein_id=WP_003103552.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA01_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA01_RS00010' for NZ_RXVW01000001.1 Protein Homology CDS 1428 2342 +
dbxref : GenBank:WP_003089829.1
gbkey : CDS
gene : mexT
id : cds-WP_003089829.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_115586225.1
locus_tag : DZA01_RS00010
name : WP_003089829.1
parent : gene-DZA01_RS00010
product : multidrug efflux system transcriptional regulator MexT
protein_id : WP_003089829.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271814/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVW01000001.1 Protein Homology CDS 1429 2343 . + 0 ID=cds-WP_003089829.1;Parent=gene-DZA01_RS00010;Dbxref=GenBank:WP_003089829.1;Name=WP_003089829.1;gbkey=CDS;gene=mexT;inference=COORDINATES: similar to AA sequence:RefSeq:WP_115586225.1;locus_tag=DZA01_RS00010;product=multidrug efflux system transcriptional regulator MexT;protein_id=WP_003089829.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA01_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA01_RS00015' for NZ_RXVW01000001.1 Protein Homology CDS 2573 3817 +
dbxref : GenBank:WP_003103549.1
gbkey : CDS
gene : mexE
id : cds-WP_003103549.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251183.1
locus_tag : DZA01_RS00015
name : WP_003103549.1
parent : gene-DZA01_RS00015
product : multidrug efflux RND transporter periplasmic adaptor subunit MexE
protein_id : WP_003103549.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271814/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVW01000001.1 Protein Homology CDS 2574 3818 . + 0 ID=cds-WP_003103549.1;Parent=gene-DZA01_RS00015;Dbxref=GenBank:WP_003103549.1;Name |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271815/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271815/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271815/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271815/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271815/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY999_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY999_RS00005' for NZ_RXVU01000001.1 Protein Homology CDS 23 511 -
dbxref : GenBank:WP_003115119.1
gbkey : CDS
gene : phzB
id : cds-WP_003115119.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250591.1
locus_tag : DY999_RS00005
name : WP_003115119.1
parent : gene-DY999_RS00005
product : phenazine biosynthesis protein PhzB
protein_id : WP_003115119.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271815/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVU01000001.1 Protein Homology CDS 24 512 . - 0 ID=cds-WP_003115119.1;Parent=gene-DY999_RS00005;Dbxref=GenBank:WP_003115119.1;Name=WP_003115119.1;gbkey=CDS;gene=phzB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250591.1;locus_tag=DY999_RS00005;product=phenazine biosynthesis protein PhzB;protein_id=WP_003115119.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY999_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY999_RS00010' for NZ_RXVU01000001.1 Protein Homology CDS 547 1035 -
dbxref : GenBank:WP_003450170.1
gbkey : CDS
gene : phzA
id : cds-WP_003450170.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250590.1
locus_tag : DY999_RS00010
name : WP_003450170.1
parent : gene-DY999_RS00010
product : phenazine biosynthesis protein PhzA
protein_id : WP_003450170.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271815/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVU01000001.1 Protein Homology CDS 548 1036 . - 0 ID=cds-WP_003450170.1;Parent=gene-DY999_RS00010;Dbxref=GenBank:WP_003450170.1;Name=WP_003450170.1;gbkey=CDS;gene=phzA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250590.1;locus_tag=DY999_RS00010;product=phenazine biosynthesis protein PhzA;protein_id=WP_003450170.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY999_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY999_RS00015' for NZ_RXVU01000001.1 Protein Homology CDS 1517 2230 -
dbxref : GenBank:WP_003118960.1
gbkey : CDS
gene : qscR
id : cds-WP_003118960.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250589.1
locus_tag : DY999_RS00015
name : WP_003118960.1
parent : gene-DY999_RS00015
product : quorum-sensing transcriptional repressor QscR
protein_id : WP_003118960.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271815/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVU01000001.1 Protein Homology CDS 1518 2231 . - 0 ID=cds-WP_003118960.1;Parent=gene-DY999_RS00015;Dbxref=GenBank:WP_003118960.1;Name=WP_003118960.1;gbkey=CDS;gene=qscR;infere |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271816/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271816/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271816/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271816/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271816/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY964_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY964_RS00010' for NZ_RXUJ01000001.1 Protein Homology CDS 258 1967 +
dbxref : GenBank:WP_126573227.1
gbkey : CDS
id : cds-WP_126573227.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250201.1
locus_tag : DY964_RS00010
name : WP_126573227.1
parent : gene-DY964_RS00010
product : esterase/lipase family protein
protein_id : WP_126573227.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271816/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUJ01000001.1 Protein Homology CDS 259 1968 . + 0 ID=cds-WP_126573227.1;Parent=gene-DY964_RS00010;Dbxref=GenBank:WP_126573227.1;Name=WP_126573227.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250201.1;locus_tag=DY964_RS00010;product=esterase/lipase family protein;protein_id=WP_126573227.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY964_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY964_RS00015' for NZ_RXUJ01000001.1 Protein Homology CDS 1964 3106 +
dbxref : GenBank:WP_003133145.1
gbkey : CDS
id : cds-WP_003133145.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250200.1
locus_tag : DY964_RS00015
name : WP_003133145.1
parent : gene-DY964_RS00015
product : T6SS immunity protein Tli4 family protein
protein_id : WP_003133145.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271816/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUJ01000001.1 Protein Homology CDS 1965 3107 . + 0 ID=cds-WP_003133145.1;Parent=gene-DY964_RS00015;Dbxref=GenBank:WP_003133145.1;Name=WP_003133145.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250200.1;locus_tag=DY964_RS00015;product=T6SS immunity protein Tli4 family protein;protein_id=WP_003133145.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY964_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY964_RS00020' for NZ_RXUJ01000001.1 Protein Homology CDS 3119 3379 +
dbxref : GenBank:WP_003083211.1
gbkey : CDS
id : cds-WP_003083211.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250199.1
locus_tag : DY964_RS00020
name : WP_003083211.1
parent : gene-DY964_RS00020
product : PAAR domain-containing protein
protein_id : WP_003083211.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271816/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXUJ01000001.1 Protein Homology CDS 3120 3380 . + 0 ID=cds-WP_003083211.1;Parent=gene-DY964_RS00020;Dbxref=GenBank:WP_003083211.1;Name=WP_003083211.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250199.1;locus_tag=DY964_RS |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271817/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271817/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271817/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271817/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271817/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY966_RS31240' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY966_RS31240' for NZ_RXUL01000001.1 Protein Homology CDS 0 84 +
dbxref : GenBank:WP_237751867.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : porin activity|0015288||IEA
go_process : carbohydrate transport|0008643||IEA
id : cds-WP_237751867.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251876.1
locus_tag : DY966_RS31240
name : WP_237751867.1
ontology_term : GO:0008643,GO:0015288,GO:0016020
parent : gene-DY966_RS31240
partial : true
product : carbohydrate porin
protein_id : WP_237751867.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271817/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUL01000001.1 Protein Homology CDS 1 85 . + 1 ID=cds-WP_237751867.1;Parent=gene-DY966_RS31240;Dbxref=GenBank:WP_237751867.1;Name=WP_237751867.1;Ontology_term=GO:0008643,GO:0015288,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=porin activity|0015288||IEA;go_process=carbohydrate transport|0008643||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251876.1;locus_tag=DY966_RS31240;partial=true;product=carbohydrate porin;protein_id=WP_237751867.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY966_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY966_RS00010' for NZ_RXUL01000001.1 Protein Homology CDS 299 1150 +
dbxref : GenBank:WP_003112064.1
gbkey : CDS
id : cds-WP_003112064.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1
locus_tag : DY966_RS00010
name : WP_003112064.1
parent : gene-DY966_RS00010
product : D-hexose-6-phosphate mutarotase
protein_id : WP_003112064.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271817/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUL01000001.1 Protein Homology CDS 300 1151 . + 0 ID=cds-WP_003112064.1;Parent=gene-DY966_RS00010;Dbxref=GenBank:WP_003112064.1;Name=WP_003112064.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015478102.1;locus_tag=DY966_RS00010;product=D-hexose-6-phosphate mutarotase;protein_id=WP_003112064.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY966_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY966_RS00015' for NZ_RXUL01000001.1 Protein Homology CDS 1159 2016 -
dbxref : GenBank:WP_003091466.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA,carbohydrate derivative binding|0097367||IEA
go_process : DNA-templated transcription|0006351||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003091466.1
inference : COORDINATES: si |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271818/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271818/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271818/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271818/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271818/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY992_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY992_RS00005' for NZ_RXVN01000001.1 Protein Homology CDS 0 384 +
dbxref : GenBank:WP_033987584.1
gbkey : CDS
id : cds-WP_033987584.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251984.1
locus_tag : DY992_RS00005
name : WP_033987584.1
parent : gene-DY992_RS00005
partial : true
product : type IV secretion protein Rhs
protein_id : WP_033987584.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271818/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVN01000001.1 Protein Homology CDS 1 385 . + 1 ID=cds-WP_033987584.1;Parent=gene-DY992_RS00005;Dbxref=GenBank:WP_033987584.1;Name=WP_033987584.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251984.1;locus_tag=DY992_RS00005;partial=true;product=type IV secretion protein Rhs;protein_id=WP_033987584.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY992_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY992_RS00010' for NZ_RXVN01000001.1 Protein Homology CDS 394 1209 +
dbxref : GenBank:WP_003138322.1
gbkey : CDS
id : cds-WP_003138322.1
inference : COORDINATES: protein motif:HMM:NF024894.5
locus_tag : DY992_RS00010
name : WP_003138322.1
parent : gene-DY992_RS00010
product : DUF4123 domain-containing protein
protein_id : WP_003138322.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271818/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVN01000001.1 Protein Homology CDS 395 1210 . + 0 ID=cds-WP_003138322.1;Parent=gene-DY992_RS00010;Dbxref=GenBank:WP_003138322.1;Name=WP_003138322.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024894.5;locus_tag=DY992_RS00010;product=DUF4123 domain-containing protein;protein_id=WP_003138322.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY992_RS32270' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY992_RS32270' for NZ_RXVN01000001.1 Protein Homology CDS 1206 1727 +
dbxref : GenBank:WP_031636319.1
gbkey : CDS
id : cds-WP_031636319.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_004351092.1
locus_tag : DY992_RS32270
name : WP_031636319.1
parent : gene-DY992_RS32270
product : DUF3304 domain-containing protein
protein_id : WP_031636319.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271818/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVN01000001.1 Protein Homology CDS 1207 1728 . + 0 ID=cds-WP_031636319.1;Parent=gene-DY992_RS32270;Dbxref=GenBank:WP_031636319.1;Name=WP_031636319.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004351092.1 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271819/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271819/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271819/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271819/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271819/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA00_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA00_RS00005' for NZ_RXVV01000001.1 Protein Homology CDS 0 423 +
dbxref : GenBank:WP_148106997.1
gbkey : CDS
go_function : efflux transmembrane transporter activity|0015562||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_148106997.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252833.1
locus_tag : DZA00_RS00005
name : WP_148106997.1
ontology_term : GO:0055085,GO:0015562
parent : gene-DZA00_RS00005
partial : true
product : TolC family protein
protein_id : WP_148106997.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271819/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVV01000001.1 Protein Homology CDS 1 424 . + 1 ID=cds-WP_148106997.1;Parent=gene-DZA00_RS00005;Dbxref=GenBank:WP_148106997.1;Name=WP_148106997.1;Ontology_term=GO:0055085,GO:0015562;gbkey=CDS;go_function=efflux transmembrane transporter activity|0015562||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252833.1;locus_tag=DZA00_RS00005;partial=true;product=TolC family protein;protein_id=WP_148106997.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA00_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA00_RS00010' for NZ_RXVV01000001.1 Protein Homology CDS 563 1582 -
dbxref : GenBank:WP_023091717.1
gbkey : CDS
gene : mexS
id : cds-WP_023091717.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251181.1
locus_tag : DZA00_RS00010
name : WP_023091717.1
parent : gene-DZA00_RS00010
product : oxidoreductase MexS
protein_id : WP_023091717.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271819/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVV01000001.1 Protein Homology CDS 564 1583 . - 0 ID=cds-WP_023091717.1;Parent=gene-DZA00_RS00010;Dbxref=GenBank:WP_023091717.1;Name=WP_023091717.1;gbkey=CDS;gene=mexS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251181.1;locus_tag=DZA00_RS00010;product=oxidoreductase MexS;protein_id=WP_023091717.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA00_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA00_RS00015' for NZ_RXVV01000001.1 Protein Homology CDS 1803 2717 +
dbxref : GenBank:WP_003089829.1
gbkey : CDS
gene : mexT
id : cds-WP_003089829.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_115586225.1
locus_tag : DZA00_RS00015
name : WP_003089829.1
parent : gene-DZA00_RS00015
product : multidrug efflux system transcriptional regulator MexT
protein_id : WP_003089829.1
source : Protein Homology
transl_table : 11 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271820/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271820/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271820/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271820/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271820/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA09_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA09_RS00005' for NZ_RXWE01000001.1 Protein Homology CDS 6 614 -
dbxref : GenBank:WP_016253925.1
gbkey : CDS
gene : msrQ
id : cds-WP_016253925.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253379.1
locus_tag : DZA09_RS00005
name : WP_016253925.1
parent : gene-DZA09_RS00005
product : protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
protein_id : WP_016253925.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271820/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWE01000001.1 Protein Homology CDS 7 615 . - 0 ID=cds-WP_016253925.1;Parent=gene-DZA09_RS00005;Dbxref=GenBank:WP_016253925.1;Name=WP_016253925.1;gbkey=CDS;gene=msrQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253379.1;locus_tag=DZA09_RS00005;product=protein-methionine-sulfoxide reductase heme-binding subunit MsrQ;protein_id=WP_016253925.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA09_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA09_RS00010' for NZ_RXWE01000001.1 Protein Homology CDS 614 1627 -
dbxref : GenBank:WP_003100146.1
gbkey : CDS
gene : msrP
go_function : oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA
go_process : protein repair|0030091||IEA
id : cds-WP_003100146.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253380.1
locus_tag : DZA09_RS00010
name : WP_003100146.1
ontology_term : GO:0030091,GO:0016667,GO:0043546
parent : gene-DZA09_RS00010
product : protein-methionine-sulfoxide reductase catalytic subunit MsrP
protein_id : WP_003100146.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271820/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWE01000001.1 Protein Homology CDS 615 1628 . - 0 ID=cds-WP_003100146.1;Parent=gene-DZA09_RS00010;Dbxref=GenBank:WP_003100146.1;Name=WP_003100146.1;Ontology_term=GO:0030091,GO:0016667,GO:0043546;gbkey=CDS;gene=msrP;go_function=oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA;go_process=protein repair|0030091||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253380.1;locus_tag=DZA09_RS00010;product=protein-methionine-sulfoxide reductase catalytic subunit MsrP;protein_id=WP_003100146.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA09_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA09_RS00015' for NZ_RXWE01000001.1 Protein Homology CDS 1688 2503 -
dbxref : GenBank:WP_003095061.1
gbkey : CDS
gene : pssA
go_function : CDP-diacylglycerol-serine O-phosphatid |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271821/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271821/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271821/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271821/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271821/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY980_RS34990' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY980_RS34990' for NZ_RXVA01000001.1 GeneMarkS-2+ CDS 0 486 +
dbxref : GenBank:WP_131201059.1
gbkey : CDS
id : cds-WP_131201059.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY980_RS34990
name : WP_131201059.1
parent : gene-DY980_RS34990
partial : true
product : hypothetical protein
protein_id : WP_131201059.1
source : GeneMarkS-2+
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271821/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVA01000001.1 GeneMarkS-2+ CDS 1 487 . + 1 ID=cds-WP_131201059.1;Parent=gene-DY980_RS34990;Dbxref=GenBank:WP_131201059.1;Name=WP_131201059.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY980_RS34990;partial=true;product=hypothetical protein;protein_id=WP_131201059.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY980_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY980_RS00020' for NZ_RXVA01000001.1 Protein Homology CDS 1147 2190 +
dbxref : GenBank:WP_016852502.1
gbkey : CDS
gene : queA
go_function : transferase activity|0016740||IEA,isomerase activity|0016853||IEA
id : cds-WP_016852502.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252513.1
locus_tag : DY980_RS00020
name : WP_016852502.1
ontology_term : GO:0016740,GO:0016853
parent : gene-DY980_RS00020
product : tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA
protein_id : WP_016852502.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271821/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RXVA01000001.1 Protein Homology CDS 1148 2191 . + 0 ID=cds-WP_016852502.1;Parent=gene-DY980_RS00020;Dbxref=GenBank:WP_016852502.1;Name=WP_016852502.1;Ontology_term=GO:0016740,GO:0016853;gbkey=CDS;gene=queA;go_function=transferase activity|0016740||IEA,isomerase activity|0016853||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252513.1;locus_tag=DY980_RS00020;product=tRNA preQ1(34) S-adenosylmethionine ribosyltransferase-isomerase QueA;protein_id=WP_016852502.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY980_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY980_RS00025' for NZ_RXVA01000001.1 Protein Homology CDS 2203 3321 +
dbxref : GenBank:WP_003100607.1
gbkey : CDS
gene : tgt
go_component : cytoplasm|0005737||IEA
go_function : tRNA-guanosine(34) queuine transglycosylase activity|0008479||IEA
go_process : tRNA modification|0006400||IEA
id : cds-WP_003100607.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252512.1
locus_tag : DY980_RS00025
name : WP_003100607.1
ontology_term : GO: |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271822/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271822/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271822/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:02 done
00:00:02 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271822/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:02 Reading file '/jetstream2/scratch/main/jobs/72271822/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA08_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA08_RS00005' for NZ_RXWD01000001.1 Protein Homology CDS 0 1357 -
dbxref : GenBank:WP_126435049.1
gbkey : CDS
id : cds-WP_126435049.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015270429.1
locus_tag : DZA08_RS00005
name : WP_126435049.1
parent : gene-DZA08_RS00005
partial : true
product : ATP-dependent nuclease
protein_id : WP_126435049.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271822/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWD01000001.1 Protein Homology CDS 1 1358 . - 0 ID=cds-WP_126435049.1;Parent=gene-DZA08_RS00005;Dbxref=GenBank:WP_126435049.1;Name=WP_126435049.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015270429.1;locus_tag=DZA08_RS00005;partial=true;product=ATP-dependent nuclease;protein_id=WP_126435049.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA08_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA08_RS00015' for NZ_RXWD01000001.1 Protein Homology CDS 2104 2460 -
dbxref : GenBank:WP_003090655.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA
id : cds-WP_003090655.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251427.2
locus_tag : DZA08_RS00015
name : WP_003090655.1
ontology_term : GO:0003677,GO:0003700
parent : gene-DZA08_RS00015
product : MerR family transcriptional regulator
protein_id : WP_003090655.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271822/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RXWD01000001.1 Protein Homology CDS 2105 2461 . - 0 ID=cds-WP_003090655.1;Parent=gene-DZA08_RS00015;Dbxref=GenBank:WP_003090655.1;Name=WP_003090655.1;Ontology_term=GO:0003677,GO:0003700;gbkey=CDS;go_function=DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251427.2;locus_tag=DZA08_RS00015;product=MerR family transcriptional regulator;protein_id=WP_003090655.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA08_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA08_RS00020' for NZ_RXWD01000001.1 Protein Homology CDS 2441 2743 -
dbxref : GenBank:WP_003090661.1
gbkey : CDS
gene : ihfA
go_function : DNA binding|0003677||IEA
go_process : DNA recombination|0006310||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003090661.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012613949.1
locus_tag : DZA08_RS00020
name : WP_003090661.1
ontology_term : GO:0006310,GO:0006355,GO:0003677
paren |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271823/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271823/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271823/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271823/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271823/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA15_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA15_RS00005' for NZ_RXWK01000001.1 Protein Homology CDS 0 384 +
dbxref : GenBank:WP_025985487.1
gbkey : CDS
id : cds-WP_025985487.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251984.1
locus_tag : DZA15_RS00005
name : WP_025985487.1
parent : gene-DZA15_RS00005
partial : true
product : Rhs element Vgr protein
protein_id : WP_025985487.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271823/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWK01000001.1 Protein Homology CDS 1 385 . + 1 ID=cds-WP_025985487.1;Parent=gene-DZA15_RS00005;Dbxref=GenBank:WP_025985487.1;Name=WP_025985487.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251984.1;locus_tag=DZA15_RS00005;partial=true;product=Rhs element Vgr protein;protein_id=WP_025985487.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA15_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA15_RS00010' for NZ_RXWK01000001.1 Protein Homology CDS 394 1209 +
dbxref : GenBank:WP_003107607.1
gbkey : CDS
id : cds-WP_003107607.1
inference : COORDINATES: protein motif:HMM:NF024894.6
locus_tag : DZA15_RS00010
name : WP_003107607.1
parent : gene-DZA15_RS00010
product : DUF4123 domain-containing protein
protein_id : WP_003107607.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271823/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWK01000001.1 Protein Homology CDS 395 1210 . + 0 ID=cds-WP_003107607.1;Parent=gene-DZA15_RS00010;Dbxref=GenBank:WP_003107607.1;Name=WP_003107607.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024894.6;locus_tag=DZA15_RS00010;product=DUF4123 domain-containing protein;protein_id=WP_003107607.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA15_RS29980' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA15_RS29980' for NZ_RXWK01000001.1 Protein Homology CDS 1206 1727 +
dbxref : GenBank:WP_004351092.1
gbkey : CDS
id : cds-WP_004351092.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_004351092.1
locus_tag : DZA15_RS29980
name : WP_004351092.1
parent : gene-DZA15_RS29980
product : DUF3304 domain-containing protein
protein_id : WP_004351092.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271823/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWK01000001.1 Protein Homology CDS 1207 1728 . + 0 ID=cds-WP_004351092.1;Parent=gene-DZA15_RS29980;Dbxref=GenBank:WP_004351092.1;Name=WP_004351092.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_004351092.1;locus_tag=DZA |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271824/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271824/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271824/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271824/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271824/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA18_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA18_RS00005' for NZ_RXWN01000001.1 Protein Homology CDS 305 3400 -
dbxref : GenBank:WP_126399537.1
gbkey : CDS
gene : dnaE2
id : cds-WP_126399537.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DZA18_RS00005
name : WP_126399537.1
parent : gene-DZA18_RS00005
product : error-prone DNA polymerase
protein_id : WP_126399537.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271824/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWN01000001.1 Protein Homology CDS 306 3401 . - 0 ID=cds-WP_126399537.1;Parent=gene-DZA18_RS00005;Dbxref=GenBank:WP_126399537.1;Name=WP_126399537.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DZA18_RS00005;product=error-prone DNA polymerase;protein_id=WP_126399537.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA18_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA18_RS00010' for NZ_RXWN01000001.1 Protein Homology CDS 3376 4791 -
dbxref : GenBank:WP_003120817.1
gbkey : CDS
id : cds-WP_003120817.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DZA18_RS00010
name : WP_003120817.1
parent : gene-DZA18_RS00010
product : Y-family DNA polymerase
protein_id : WP_003120817.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271824/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWN01000001.1 Protein Homology CDS 3377 4792 . - 0 ID=cds-WP_003120817.1;Parent=gene-DZA18_RS00010;Dbxref=GenBank:WP_003120817.1;Name=WP_003120817.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DZA18_RS00010;product=Y-family DNA polymerase;protein_id=WP_003120817.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA18_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA18_RS00015' for NZ_RXWN01000001.1 Protein Homology CDS 4799 5404 -
dbxref : GenBank:WP_031639058.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031639058.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_014820649.1
locus_tag : DZA18_RS00015
name : WP_031639058.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DZA18_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031639058.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271824/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWN01000001.1 Protein Homology CDS 4800 5405 . - 0 ID=cds-WP_031639058.1;Parent=gene-DZA18_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271825/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271825/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271825/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271825/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271825/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA22_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA22_RS00005' for NZ_RXWR01000001.1 Protein Homology CDS 0 1176 -
dbxref : GenBank:WP_217989941.1
end_range : 1177,.
gbkey : CDS
gene : oprB
id : cds-WP_217989941.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251876.1
locus_tag : DZA22_RS00005
name : WP_217989941.1
parent : gene-DZA22_RS00005
partial : true
product : carbohydrate porin
protein_id : WP_217989941.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271825/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWR01000001.1 Protein Homology CDS 1 1177 . - 0 ID=cds-WP_217989941.1;Parent=gene-DZA22_RS00005;Dbxref=GenBank:WP_217989941.1;Name=WP_217989941.1;end_range=1177,.;gbkey=CDS;gene=oprB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251876.1;locus_tag=DZA22_RS00005;partial=true;product=carbohydrate porin;protein_id=WP_217989941.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA22_RS30465' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA22_RS30465' for NZ_RXWR01000002.1 Protein Homology CDS 0 107 -
dbxref : GenBank:WP_223818285.1
gbkey : CDS
id : cds-WP_223818285.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251876.1
locus_tag : DZA22_RS30465
name : WP_223818285.1
parent : gene-DZA22_RS30465
partial : true
product : hypothetical protein
protein_id : WP_223818285.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271825/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RXWR01000002.1 Protein Homology CDS 1 108 . - 0 ID=cds-WP_223818285.1;Parent=gene-DZA22_RS30465;Dbxref=GenBank:WP_223818285.1;Name=WP_223818285.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251876.1;locus_tag=DZA22_RS30465;partial=true;product=hypothetical protein;protein_id=WP_223818285.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA22_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA22_RS00010' for NZ_RXWR01000002.1 Protein Homology CDS 151 1311 -
dbxref : GenBank:WP_003119710.1
gbkey : CDS
go_function : ATP binding|0005524||IEA,ATP hydrolysis activity|0016887||IEA,ATPase-coupled transmembrane transporter activity|0042626||IEA,ABC-type transporter activity|0140359||IEA
id : cds-WP_003119710.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251877.1
locus_tag : DZA22_RS00010
name : WP_003119710.1
ontology_term : GO:0005524,GO:0016887,GO:0042626,GO:0140359
parent : gene-DZA22_RS00010
product : ABC transporter ATP-binding protein
protein_id : WP_003119710.1
source : Protein Homology
transl_table : 11
type |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271826/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271826/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271826/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271826/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271826/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA10_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA10_RS00005' for NZ_RXWF01000001.1 Protein Homology CDS 282 3377 -
dbxref : GenBank:WP_079279355.1
gbkey : CDS
gene : dnaE2
id : cds-WP_079279355.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DZA10_RS00005
name : WP_079279355.1
parent : gene-DZA10_RS00005
product : error-prone DNA polymerase
protein_id : WP_079279355.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271826/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWF01000001.1 Protein Homology CDS 283 3378 . - 0 ID=cds-WP_079279355.1;Parent=gene-DZA10_RS00005;Dbxref=GenBank:WP_079279355.1;Name=WP_079279355.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DZA10_RS00005;product=error-prone DNA polymerase;protein_id=WP_079279355.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA10_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA10_RS00010' for NZ_RXWF01000001.1 Protein Homology CDS 3353 4768 -
dbxref : GenBank:WP_003116540.1
gbkey : CDS
id : cds-WP_003116540.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DZA10_RS00010
name : WP_003116540.1
parent : gene-DZA10_RS00010
product : DNA polymerase Y family protein
protein_id : WP_003116540.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271826/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWF01000001.1 Protein Homology CDS 3354 4769 . - 0 ID=cds-WP_003116540.1;Parent=gene-DZA10_RS00010;Dbxref=GenBank:WP_003116540.1;Name=WP_003116540.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DZA10_RS00010;product=DNA polymerase Y family protein;protein_id=WP_003116540.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA10_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA10_RS00015' for NZ_RXWF01000001.1 Protein Homology CDS 4776 5420 -
dbxref : GenBank:WP_042115121.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_042115121.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_017245657.1
locus_tag : DZA10_RS00015
name : WP_042115121.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DZA10_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_042115121.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271826/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWF01000001.1 Protein Homology CDS 4777 5421 . - 0 ID=cds-WP_042115121.1 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271827/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271827/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271827/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271827/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271827/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA13_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA13_RS00005' for NZ_RXWI01000001.1 Protein Homology CDS 6 614 -
dbxref : GenBank:WP_016253925.1
gbkey : CDS
gene : msrQ
id : cds-WP_016253925.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253379.1
locus_tag : DZA13_RS00005
name : WP_016253925.1
parent : gene-DZA13_RS00005
product : protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
protein_id : WP_016253925.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271827/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWI01000001.1 Protein Homology CDS 7 615 . - 0 ID=cds-WP_016253925.1;Parent=gene-DZA13_RS00005;Dbxref=GenBank:WP_016253925.1;Name=WP_016253925.1;gbkey=CDS;gene=msrQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253379.1;locus_tag=DZA13_RS00005;product=protein-methionine-sulfoxide reductase heme-binding subunit MsrQ;protein_id=WP_016253925.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA13_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA13_RS00010' for NZ_RXWI01000001.1 Protein Homology CDS 614 1627 -
dbxref : GenBank:WP_004352658.1
gbkey : CDS
gene : msrP
go_function : oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA
go_process : protein repair|0030091||IEA
id : cds-WP_004352658.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253380.1
locus_tag : DZA13_RS00010
name : WP_004352658.1
ontology_term : GO:0030091,GO:0016667,GO:0043546
parent : gene-DZA13_RS00010
product : protein-methionine-sulfoxide reductase catalytic subunit MsrP
protein_id : WP_004352658.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271827/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWI01000001.1 Protein Homology CDS 615 1628 . - 0 ID=cds-WP_004352658.1;Parent=gene-DZA13_RS00010;Dbxref=GenBank:WP_004352658.1;Name=WP_004352658.1;Ontology_term=GO:0030091,GO:0016667,GO:0043546;gbkey=CDS;gene=msrP;go_function=oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA;go_process=protein repair|0030091||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253380.1;locus_tag=DZA13_RS00010;product=protein-methionine-sulfoxide reductase catalytic subunit MsrP;protein_id=WP_004352658.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA13_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA13_RS00015' for NZ_RXWI01000001.1 Protein Homology CDS 1688 2503 -
dbxref : GenBank:WP_003095061.1
gbkey : CDS
gene : pssA
go_function : CDP-diacylglycerol-serine O-phosphatid |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271828/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271828/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271828/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271828/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271828/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA21_RS32295' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA21_RS32295' for NZ_RXWQ01000001.1 GeneMarkS-2+ CDS 0 323 +
dbxref : GenBank:WP_221768286.1
gbkey : CDS
id : cds-WP_221768286.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DZA21_RS32295
name : WP_221768286.1
parent : gene-DZA21_RS32295
partial : true
product : hypothetical protein
protein_id : WP_221768286.1
source : GeneMarkS-2+
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271828/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWQ01000001.1 GeneMarkS-2+ CDS 1 324 . + 0 ID=cds-WP_221768286.1;Parent=gene-DZA21_RS32295;Dbxref=GenBank:WP_221768286.1;Name=WP_221768286.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DZA21_RS32295;partial=true;product=hypothetical protein;protein_id=WP_221768286.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA21_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA21_RS00005' for NZ_RXWQ01000001.1 Protein Homology CDS 272 1588 -
dbxref : GenBank:WP_015503859.1
gbkey : CDS
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_015503859.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254057.1
locus_tag : DZA21_RS00005
name : WP_015503859.1
ontology_term : GO:0055085,GO:0022857
parent : gene-DZA21_RS00005
product : MFS transporter
protein_id : WP_015503859.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271828/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWQ01000001.1 Protein Homology CDS 273 1589 . - 0 ID=cds-WP_015503859.1;Parent=gene-DZA21_RS00005;Dbxref=GenBank:WP_015503859.1;Name=WP_015503859.1;Ontology_term=GO:0055085,GO:0022857;gbkey=CDS;go_function=transmembrane transporter activity|0022857||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254057.1;locus_tag=DZA21_RS00005;product=MFS transporter;protein_id=WP_015503859.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA21_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA21_RS00010' for NZ_RXWQ01000001.1 Protein Homology CDS 1876 2280 +
dbxref : GenBank:WP_003096677.1
gbkey : CDS
go_function : fatty acyl-CoA hydrolase activity|0047617||IEA
id : cds-WP_003096677.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254058.1
locus_tag : DZA21_RS00010
name : WP_003096677.1
ontology_term : GO:0047617
parent : gene-DZA21_RS00010
product : acyl-CoA thioesterase
protein_id : WP_003096677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scr |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271829/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271829/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271829/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271829/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271829/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA20_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA20_RS00005' for NZ_RXWP01000001.1 Protein Homology CDS 49 777 +
dbxref : GenBank:WP_003146164.1
gbkey : CDS
id : cds-WP_003146164.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253486.1
locus_tag : DZA20_RS00005
name : WP_003146164.1
parent : gene-DZA20_RS00005
product : GrpB family protein
protein_id : WP_003146164.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271829/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWP01000001.1 Protein Homology CDS 50 778 . + 0 ID=cds-WP_003146164.1;Parent=gene-DZA20_RS00005;Dbxref=GenBank:WP_003146164.1;Name=WP_003146164.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253486.1;locus_tag=DZA20_RS00005;product=GrpB family protein;protein_id=WP_003146164.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA20_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA20_RS00010' for NZ_RXWP01000001.1 GeneMarkS-2+ CDS 800 1405 -
dbxref : GenBank:WP_196493974.1
gbkey : CDS
id : cds-WP_196493974.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DZA20_RS00010
name : WP_196493974.1
parent : gene-DZA20_RS00010
product : AAA family ATPase
protein_id : WP_196493974.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271829/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWP01000001.1 GeneMarkS-2+ CDS 801 1406 . - 0 ID=cds-WP_196493974.1;Parent=gene-DZA20_RS00010;Dbxref=GenBank:WP_196493974.1;Name=WP_196493974.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DZA20_RS00010;product=AAA family ATPase;protein_id=WP_196493974.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA20_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA20_RS00015' for NZ_RXWP01000001.1 Protein Homology CDS 1375 2175 -
dbxref : GenBank:WP_003095295.1
gbkey : CDS
go_function : 2-polyprenyl-6-methoxy-1%2C4-benzoquinone methyltransferase activity|0008425||IEA,3-demethylubiquinol-n 3-O-methyltransferase activity|0061542||IEA,2-polyprenyl-6-hydroxyphenol methylase activity|0102208||IEA
go_process : ubiquinone biosynthetic process|0006744||IEA,methylation|0032259||IEA
id : cds-WP_003095295.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253488.1
locus_tag : DZA20_RS00015
name : WP_003095295.1
ontology_term : GO:0006744,GO:0032259,GO:0008425,GO:0061542,GO:0102208
parent : gene-DZA20_RS00015
product : class I SAM-dependent methyltransferase
protein_id : WP_003095295.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271829/working/snpeff_output/Pseudo |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271830/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271830/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271830/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271830/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271830/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB92_RS35670' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB92_RS35670' for NZ_PSQQ01000001.1 GeneMarkS-2+ CDS 262 633 +
dbxref : GenBank:WP_235180845.1
gbkey : CDS
id : cds-WP_235180845.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSB92_RS35670
name : WP_235180845.1
parent : gene-CSB92_RS35670
product : hypothetical protein
protein_id : WP_235180845.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271830/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_PSQQ01000001.1 GeneMarkS-2+ CDS 263 634 . + 0 ID=cds-WP_235180845.1;Parent=gene-CSB92_RS35670;Dbxref=GenBank:WP_235180845.1;Name=WP_235180845.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSB92_RS35670;product=hypothetical protein;protein_id=WP_235180845.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB92_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB92_RS00010' for NZ_PSQQ01000001.1 GeneMarkS-2+ CDS 680 874 +
dbxref : GenBank:WP_003094256.1
gbkey : CDS
id : cds-WP_003094256.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSB92_RS00010
name : WP_003094256.1
parent : gene-CSB92_RS00010
product : hypothetical protein
protein_id : WP_003094256.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271830/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_PSQQ01000001.1 GeneMarkS-2+ CDS 681 875 . + 0 ID=cds-WP_003094256.1;Parent=gene-CSB92_RS00010;Dbxref=GenBank:WP_003094256.1;Name=WP_003094256.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSB92_RS00010;product=hypothetical protein;protein_id=WP_003094256.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB92_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB92_RS00015' for NZ_PSQQ01000001.1 Protein Homology CDS 874 1200 +
dbxref : GenBank:WP_003094258.1
gbkey : CDS
id : cds-WP_003094258.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003094258.1
locus_tag : CSB92_RS00015
name : WP_003094258.1
parent : gene-CSB92_RS00015
product : Acb2/Tad1 domain-containing protein
protein_id : WP_003094258.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271830/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_PSQQ01000001.1 Protein Homology CDS 875 1201 . + 0 ID=cds-WP_003094258.1;Parent=gene-CSB92_RS00015;Dbxref=GenBank:WP_003094258.1;Name=WP_003094258.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003094258.1;locus_tag=CSB92_RS00015;product=Acb2/Tad1 domain-containing protein;protein_id=WP_003094258.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's p |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271831/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271831/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271831/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271831/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271831/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY972_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY972_RS00010' for NZ_RXUR01000001.1 GeneMarkS-2+ CDS 405 1460 +
dbxref : GenBank:WP_031655160.1
gbkey : CDS
id : cds-WP_031655160.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY972_RS00010
name : WP_031655160.1
parent : gene-DY972_RS00010
product : hypothetical protein
protein_id : WP_031655160.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271831/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUR01000001.1 GeneMarkS-2+ CDS 406 1461 . + 0 ID=cds-WP_031655160.1;Parent=gene-DY972_RS00010;Dbxref=GenBank:WP_031655160.1;Name=WP_031655160.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY972_RS00010;product=hypothetical protein;protein_id=WP_031655160.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY972_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY972_RS00015' for NZ_RXUR01000001.1 GeneMarkS-2+ CDS 1609 2199 -
dbxref : GenBank:WP_023083336.1
gbkey : CDS
id : cds-WP_023083336.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY972_RS00015
name : WP_023083336.1
parent : gene-DY972_RS00015
product : hypothetical protein
protein_id : WP_023083336.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271831/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUR01000001.1 GeneMarkS-2+ CDS 1610 2200 . - 0 ID=cds-WP_023083336.1;Parent=gene-DY972_RS00015;Dbxref=GenBank:WP_023083336.1;Name=WP_023083336.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY972_RS00015;product=hypothetical protein;protein_id=WP_023083336.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY972_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY972_RS00020' for NZ_RXUR01000001.1 GeneMarkS-2+ CDS 2207 2920 -
dbxref : GenBank:WP_023083337.1
gbkey : CDS
id : cds-WP_023083337.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY972_RS00020
name : WP_023083337.1
parent : gene-DY972_RS00020
product : hypothetical protein
protein_id : WP_023083337.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271831/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUR01000001.1 GeneMarkS-2+ CDS 2208 2921 . - 0 ID=cds-WP_023083337.1;Parent=gene-DY972_RS00020;Dbxref=GenBank:WP_023083337.1;Name=WP_023083337.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY972_RS00020;product=hypothetical protein;protein_id=WP_023083337.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY972_RS00025' is a Gene instead of a trans |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271832/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271832/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271832/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271832/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271832/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY984_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY984_RS00005' for NZ_RXVF01000001.1 Protein Homology CDS 0 282 +
dbxref : GenBank:WP_148112582.1
gbkey : CDS
id : cds-WP_148112582.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_076611480.1
locus_tag : DY984_RS00005
name : WP_148112582.1
parent : gene-DY984_RS00005
partial : true
product : integrase core domain-containing protein
protein_id : WP_148112582.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271832/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVF01000001.1 Protein Homology CDS 1 283 . + 1 ID=cds-WP_148112582.1;Parent=gene-DY984_RS00005;Dbxref=GenBank:WP_148112582.1;Name=WP_148112582.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_076611480.1;locus_tag=DY984_RS00005;partial=true;product=integrase core domain-containing protein;protein_id=WP_148112582.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY984_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY984_RS00010' for NZ_RXVF01000001.1 Protein Homology CDS 700 1149 -
dbxref : GenBank:WP_126885698.1
gbkey : CDS
id : cds-WP_126885698.1
inference : COORDINATES: protein motif:HMM:NF037740.5
locus_tag : DY984_RS00010
name : WP_126885698.1
parent : gene-DY984_RS00010
product : hypothetical protein
protein_id : WP_126885698.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271832/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVF01000001.1 Protein Homology CDS 701 1150 . - 0 ID=cds-WP_126885698.1;Parent=gene-DY984_RS00010;Dbxref=GenBank:WP_126885698.1;Name=WP_126885698.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF037740.5;locus_tag=DY984_RS00010;product=hypothetical protein;protein_id=WP_126885698.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY984_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY984_RS00015' for NZ_RXVF01000001.1 GeneMarkS-2+ CDS 1151 1615 -
dbxref : GenBank:WP_201267248.1
gbkey : CDS
id : cds-WP_201267248.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY984_RS00015
name : WP_201267248.1
parent : gene-DY984_RS00015
product : hypothetical protein
protein_id : WP_201267248.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271832/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVF01000001.1 GeneMarkS-2+ CDS 1152 1616 . - 0 ID=cds-WP_201267248.1;Parent=gene-DY984_RS00015;Dbxref=GenBank:WP_201267248.1;Name=WP_201267248.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY984_RS00015;product=hypothetical protein; |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271833/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271833/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271833/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271833/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271833/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY988_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY988_RS00005' for NZ_RXVJ01000001.1 Protein Homology CDS 0 708 +
dbxref : GenBank:WP_019416291.1
gbkey : CDS
id : cds-WP_019416291.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250202.1
locus_tag : DY988_RS00005
name : WP_019416291.1
parent : gene-DY988_RS00005
partial : true
product : DUF2345 domain-containing protein
protein_id : WP_019416291.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271833/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVJ01000001.1 Protein Homology CDS 1 709 . + 1 ID=cds-WP_019416291.1;Parent=gene-DY988_RS00005;Dbxref=GenBank:WP_019416291.1;Name=WP_019416291.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250202.1;locus_tag=DY988_RS00005;partial=true;product=DUF2345 domain-containing protein;protein_id=WP_019416291.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY988_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY988_RS00010' for NZ_RXVJ01000001.1 Protein Homology CDS 705 2411 +
dbxref : GenBank:WP_003117782.1
gbkey : CDS
id : cds-WP_003117782.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250201.1
locus_tag : DY988_RS00010
name : WP_003117782.1
parent : gene-DY988_RS00010
product : esterase/lipase family protein
protein_id : WP_003117782.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271833/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVJ01000001.1 Protein Homology CDS 706 2412 . + 0 ID=cds-WP_003117782.1;Parent=gene-DY988_RS00010;Dbxref=GenBank:WP_003117782.1;Name=WP_003117782.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250201.1;locus_tag=DY988_RS00010;product=esterase/lipase family protein;protein_id=WP_003117782.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY988_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY988_RS00015' for NZ_RXVJ01000001.1 Protein Homology CDS 2408 3553 +
dbxref : GenBank:WP_031633157.1
gbkey : CDS
id : cds-WP_031633157.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003083213.1
locus_tag : DY988_RS00015
name : WP_031633157.1
parent : gene-DY988_RS00015
product : T6SS immunity protein Tli4 family protein
protein_id : WP_031633157.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271833/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVJ01000001.1 Protein Homology CDS 2409 3554 . + 0 ID=cds-WP_031633157.1;Parent=gene-DY988_RS00015;Dbxref=GenBank:WP_031633157.1;Name=WP_031633157.1;gbkey=CDS;inference=COORDINATES: similar |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271834/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271834/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271834/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271834/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271834/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA17_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA17_RS00005' for NZ_RXWM01000001.1 Protein Homology CDS 0 522 +
dbxref : GenBank:WP_148107419.1
gbkey : CDS
id : cds-WP_148107419.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253421.1
locus_tag : DZA17_RS00005
name : WP_148107419.1
parent : gene-DZA17_RS00005
partial : true
product : AMP-binding enzyme
protein_id : WP_148107419.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271834/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXWM01000001.1 Protein Homology CDS 1 523 . + 1 ID=cds-WP_148107419.1;Parent=gene-DZA17_RS00005;Dbxref=GenBank:WP_148107419.1;Name=WP_148107419.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253421.1;locus_tag=DZA17_RS00005;partial=true;product=AMP-binding enzyme;protein_id=WP_148107419.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA17_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA17_RS00010' for NZ_RXWM01000001.1 Protein Homology CDS 620 1501 +
dbxref : GenBank:WP_003113910.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA
id : cds-WP_003113910.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253422.1
locus_tag : DZA17_RS00010
name : WP_003113910.1
ontology_term : GO:0016491
parent : gene-DZA17_RS00010
product : oxygenase MpaB family protein
protein_id : WP_003113910.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271834/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWM01000001.1 Protein Homology CDS 621 1502 . + 0 ID=cds-WP_003113910.1;Parent=gene-DZA17_RS00010;Dbxref=GenBank:WP_003113910.1;Name=WP_003113910.1;Ontology_term=GO:0016491;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253422.1;locus_tag=DZA17_RS00010;product=oxygenase MpaB family protein;protein_id=WP_003113910.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA17_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA17_RS00015' for NZ_RXWM01000001.1 Protein Homology CDS 1626 4892 +
dbxref : GenBank:WP_015648004.1
gbkey : CDS
id : cds-WP_015648004.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253423.1
locus_tag : DZA17_RS00015
name : WP_015648004.1
parent : gene-DZA17_RS00015
product : DUF748 domain-containing protein
protein_id : WP_015648004.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271834/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWM01000001.1 Protein Homology CDS 1627 4893 . + 0 ID=cds-WP_015648004.1;Paren |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271835/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271835/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271835/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271835/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271835/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY982_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY982_RS00005' for NZ_RXVC01000001.1 Protein Homology CDS 35 523 -
dbxref : GenBank:WP_003123955.1
gbkey : CDS
gene : phzB
id : cds-WP_003123955.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252900.1
locus_tag : DY982_RS00005
name : WP_003123955.1
parent : gene-DY982_RS00005
product : phenazine biosynthesis protein PhzB
protein_id : WP_003123955.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271835/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVC01000001.1 Protein Homology CDS 36 524 . - 0 ID=cds-WP_003123955.1;Parent=gene-DY982_RS00005;Dbxref=GenBank:WP_003123955.1;Name=WP_003123955.1;gbkey=CDS;gene=phzB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252900.1;locus_tag=DY982_RS00005;product=phenazine biosynthesis protein PhzB;protein_id=WP_003123955.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY982_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY982_RS00010' for NZ_RXVC01000001.1 Protein Homology CDS 553 1041 -
dbxref : GenBank:WP_012613549.1
gbkey : CDS
gene : phzA
id : cds-WP_012613549.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252899.1
locus_tag : DY982_RS00010
name : WP_012613549.1
parent : gene-DY982_RS00010
product : phenazine biosynthesis protein PhzA
protein_id : WP_012613549.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271835/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVC01000001.1 Protein Homology CDS 554 1042 . - 0 ID=cds-WP_012613549.1;Parent=gene-DY982_RS00010;Dbxref=GenBank:WP_012613549.1;Name=WP_012613549.1;gbkey=CDS;gene=phzA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252899.1;locus_tag=DY982_RS00010;product=phenazine biosynthesis protein PhzA;protein_id=WP_012613549.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY982_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY982_RS00020' for NZ_RXVC01000001.1 Protein Homology CDS 1738 2742 +
dbxref : GenBank:WP_003093617.1
gbkey : CDS
gene : phzM
id : cds-WP_003093617.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252898.1
locus_tag : DY982_RS00020
name : WP_003093617.1
parent : gene-DY982_RS00020
product : phenazine-1-carboxylate N-methyltransferase PhzM
protein_id : WP_003093617.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271835/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVC01000001.1 Protein Homology CDS 1739 2743 . + 0 ID=cds-WP_003093617.1;Parent=gene-DY982_RS00020;Dbxref=GenBank:WP_003093617.1;Name=WP_003093617.1;gbkey=CDS;gene=phzM;infe |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271836/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271836/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271836/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271836/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271836/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY975_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY975_RS00005' for NZ_RXUU01000001.1 Protein Homology CDS 188 1207 -
dbxref : GenBank:WP_003103552.1
gbkey : CDS
gene : mexS
id : cds-WP_003103552.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251181.1
locus_tag : DY975_RS00005
name : WP_003103552.1
parent : gene-DY975_RS00005
product : oxidoreductase MexS
protein_id : WP_003103552.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271836/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUU01000001.1 Protein Homology CDS 189 1208 . - 0 ID=cds-WP_003103552.1;Parent=gene-DY975_RS00005;Dbxref=GenBank:WP_003103552.1;Name=WP_003103552.1;gbkey=CDS;gene=mexS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251181.1;locus_tag=DY975_RS00005;product=oxidoreductase MexS;protein_id=WP_003103552.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY975_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY975_RS00010' for NZ_RXUU01000001.1 Protein Homology CDS 1428 2342 +
dbxref : GenBank:WP_003089829.1
gbkey : CDS
gene : mexT
id : cds-WP_003089829.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_115586225.1
locus_tag : DY975_RS00010
name : WP_003089829.1
parent : gene-DY975_RS00010
product : multidrug efflux system transcriptional regulator MexT
protein_id : WP_003089829.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271836/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUU01000001.1 Protein Homology CDS 1429 2343 . + 0 ID=cds-WP_003089829.1;Parent=gene-DY975_RS00010;Dbxref=GenBank:WP_003089829.1;Name=WP_003089829.1;gbkey=CDS;gene=mexT;inference=COORDINATES: similar to AA sequence:RefSeq:WP_115586225.1;locus_tag=DY975_RS00010;product=multidrug efflux system transcriptional regulator MexT;protein_id=WP_003089829.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY975_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY975_RS00015' for NZ_RXUU01000001.1 Protein Homology CDS 2573 3817 +
dbxref : GenBank:WP_003103549.1
gbkey : CDS
gene : mexE
id : cds-WP_003103549.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251183.1
locus_tag : DY975_RS00015
name : WP_003103549.1
parent : gene-DY975_RS00015
product : multidrug efflux RND transporter periplasmic adaptor subunit MexE
protein_id : WP_003103549.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271836/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUU01000001.1 Protein Homology CDS 2574 3818 . + 0 ID=cds-WP_003103549.1;Parent=gene-DY975_RS00015;Dbxref=GenBank:WP_003103549.1;Name |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271837/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271837/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271837/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271837/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271837/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY994_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY994_RS00005' for NZ_RXVP01000001.1 Protein Homology CDS 294 3389 -
dbxref : GenBank:WP_079388431.1
gbkey : CDS
gene : dnaE2
id : cds-WP_079388431.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY994_RS00005
name : WP_079388431.1
parent : gene-DY994_RS00005
product : error-prone DNA polymerase
protein_id : WP_079388431.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271837/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVP01000001.1 Protein Homology CDS 295 3390 . - 0 ID=cds-WP_079388431.1;Parent=gene-DY994_RS00005;Dbxref=GenBank:WP_079388431.1;Name=WP_079388431.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY994_RS00005;product=error-prone DNA polymerase;protein_id=WP_079388431.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY994_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY994_RS00010' for NZ_RXVP01000001.1 Protein Homology CDS 3365 4780 -
dbxref : GenBank:WP_003455174.1
gbkey : CDS
id : cds-WP_003455174.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY994_RS00010
name : WP_003455174.1
parent : gene-DY994_RS00010
product : Y-family DNA polymerase
protein_id : WP_003455174.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271837/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVP01000001.1 Protein Homology CDS 3366 4781 . - 0 ID=cds-WP_003455174.1;Parent=gene-DY994_RS00010;Dbxref=GenBank:WP_003455174.1;Name=WP_003455174.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY994_RS00010;product=Y-family DNA polymerase;protein_id=WP_003455174.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY994_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY994_RS00015' for NZ_RXVP01000001.1 Protein Homology CDS 4788 5393 -
dbxref : GenBank:WP_031627677.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031627677.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003296675.1
locus_tag : DY994_RS00015
name : WP_031627677.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY994_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031627677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271837/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXVP01000001.1 Protein Homology CDS 4789 5394 . - 0 ID=cds-WP_031627677.1;Parent=gene-DY994_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271838/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271838/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271838/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271838/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271838/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA24_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA24_RS00005' for NZ_RXVE01000001.1 Protein Homology CDS 1 609 -
dbxref : GenBank:WP_003116064.1
gbkey : CDS
gene : msrQ
id : cds-WP_003116064.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253379.1
locus_tag : DZA24_RS00005
name : WP_003116064.1
parent : gene-DZA24_RS00005
product : protein-methionine-sulfoxide reductase heme-binding subunit MsrQ
protein_id : WP_003116064.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271838/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVE01000001.1 Protein Homology CDS 2 610 . - 0 ID=cds-WP_003116064.1;Parent=gene-DZA24_RS00005;Dbxref=GenBank:WP_003116064.1;Name=WP_003116064.1;gbkey=CDS;gene=msrQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253379.1;locus_tag=DZA24_RS00005;product=protein-methionine-sulfoxide reductase heme-binding subunit MsrQ;protein_id=WP_003116064.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA24_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA24_RS00010' for NZ_RXVE01000001.1 Protein Homology CDS 609 1622 -
dbxref : GenBank:WP_003100146.1
gbkey : CDS
gene : msrP
go_function : oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA
go_process : protein repair|0030091||IEA
id : cds-WP_003100146.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253380.1
locus_tag : DZA24_RS00010
name : WP_003100146.1
ontology_term : GO:0030091,GO:0016667,GO:0043546
parent : gene-DZA24_RS00010
product : protein-methionine-sulfoxide reductase catalytic subunit MsrP
protein_id : WP_003100146.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271838/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVE01000001.1 Protein Homology CDS 610 1623 . - 0 ID=cds-WP_003100146.1;Parent=gene-DZA24_RS00010;Dbxref=GenBank:WP_003100146.1;Name=WP_003100146.1;Ontology_term=GO:0030091,GO:0016667,GO:0043546;gbkey=CDS;gene=msrP;go_function=oxidoreductase activity%2C acting on a sulfur group of donors|0016667||IEA,molybdopterin cofactor binding|0043546||IEA;go_process=protein repair|0030091||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253380.1;locus_tag=DZA24_RS00010;product=protein-methionine-sulfoxide reductase catalytic subunit MsrP;protein_id=WP_003100146.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA24_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA24_RS00015' for NZ_RXVE01000001.1 Protein Homology CDS 1683 2498 -
dbxref : GenBank:WP_003095061.1
gbkey : CDS
gene : pssA
go_function : CDP-diacylglycerol-serine O-phosphatid |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271839/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271839/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271839/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271839/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271839/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA07_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA07_RS00010' for NZ_RXWC01000001.1 Protein Homology CDS 575 1093 +
dbxref : GenBank:WP_003108870.1
gbkey : CDS
id : cds-WP_003108870.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251440.1
locus_tag : DZA07_RS00010
name : WP_003108870.1
parent : gene-DZA07_RS00010
product : thermonuclease family protein
protein_id : WP_003108870.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271839/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXWC01000001.1 Protein Homology CDS 576 1094 . + 0 ID=cds-WP_003108870.1;Parent=gene-DZA07_RS00010;Dbxref=GenBank:WP_003108870.1;Name=WP_003108870.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251440.1;locus_tag=DZA07_RS00010;product=thermonuclease family protein;protein_id=WP_003108870.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA07_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA07_RS00015' for NZ_RXWC01000001.1 Protein Homology CDS 1068 1298 -
dbxref : GenBank:WP_003090795.1
gbkey : CDS
id : cds-WP_003090795.1
inference : COORDINATES: similar to AA sequence:RefSeq:YP_008719758.1
locus_tag : DZA07_RS00015
name : WP_003090795.1
parent : gene-DZA07_RS00015
product : hypothetical protein
protein_id : WP_003090795.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271839/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXWC01000001.1 Protein Homology CDS 1069 1299 . - 0 ID=cds-WP_003090795.1;Parent=gene-DZA07_RS00015;Dbxref=GenBank:WP_003090795.1;Name=WP_003090795.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:YP_008719758.1;locus_tag=DZA07_RS00015;product=hypothetical protein;protein_id=WP_003090795.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DZA07_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DZA07_RS00020' for NZ_RXWC01000001.1 Protein Homology CDS 1364 1597 -
dbxref : GenBank:WP_003090796.1
gbkey : CDS
id : cds-WP_003090796.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_016253316.1
locus_tag : DZA07_RS00020
name : WP_003090796.1
parent : gene-DZA07_RS00020
product : DUF3509 domain-containing protein
protein_id : WP_003090796.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271839/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXWC01000001.1 Protein Homology CDS 1365 1598 . - 0 ID=cds-WP_003090796.1;Parent=gene-DZA07_RS00020;Dbxref=GenBank:WP_003090796.1;Name=WP_003090796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016253316.1;locus_tag=DZA07_RS00020;product=DUF3509 domain-contain |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271840/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271840/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271840/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271840/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271840/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY993_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY993_RS00010' for NZ_RXVO01000001.1 Protein Homology CDS 110 541 -
dbxref : GenBank:WP_078451886.1
gbkey : CDS
id : cds-WP_078451886.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003151445.1
locus_tag : DY993_RS00010
name : WP_078451886.1
parent : gene-DY993_RS00010
product : TIGR03757 family integrating conjugative element protein
protein_id : WP_078451886.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271840/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVO01000001.1 Protein Homology CDS 111 542 . - 0 ID=cds-WP_078451886.1;Parent=gene-DY993_RS00010;Dbxref=GenBank:WP_078451886.1;Name=WP_078451886.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003151445.1;locus_tag=DY993_RS00010;product=TIGR03757 family integrating conjugative element protein;protein_id=WP_078451886.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY993_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY993_RS00025' for NZ_RXVO01000001.1 Protein Homology CDS 2663 2881 +
dbxref : GenBank:WP_003108468.1
gbkey : CDS
id : cds-WP_003108468.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_016264198.1
locus_tag : DY993_RS00025
name : WP_003108468.1
parent : gene-DY993_RS00025
product : hypothetical protein
protein_id : WP_003108468.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271840/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVO01000001.1 Protein Homology CDS 2664 2882 . + 0 ID=cds-WP_003108468.1;Parent=gene-DY993_RS00025;Dbxref=GenBank:WP_003108468.1;Name=WP_003108468.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016264198.1;locus_tag=DY993_RS00025;product=hypothetical protein;protein_id=WP_003108468.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY993_RS00035' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY993_RS00035' for NZ_RXVO01000001.1 Protein Homology CDS 3095 3544 +
dbxref : GenBank:WP_015503379.1
gbkey : CDS
go_function : N-acetyltransferase activity|0008080||IEA,acyltransferase activity|0016746||IEA
id : cds-WP_015503379.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015503379.1
locus_tag : DY993_RS00035
name : WP_015503379.1
ontology_term : GO:0008080,GO:0016746
parent : gene-DY993_RS00035
product : GNAT family N-acetyltransferase
protein_id : WP_015503379.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271840/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXVO01000001.1 Protein Homology CDS 3096 3545 . + 0 ID=cds-WP_015503379.1;Parent=gene |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271841/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271841/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271841/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271841/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271841/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY927_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY927_RS00005' for NZ_RXSY01000001.1 Protein Homology CDS 0 492 +
dbxref : GenBank:WP_021204922.1
end_range : 493,.
gbkey : CDS
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_021204922.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248954.1
locus_tag : DY927_RS00005
name : WP_021204922.1
ontology_term : GO:0033103
parent : gene-DY927_RS00005
partial : true
product : Hcp family type VI secretion system effector
protein_id : WP_021204922.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271841/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXSY01000001.1 Protein Homology CDS 1 493 . + 0 ID=cds-WP_021204922.1;Parent=gene-DY927_RS00005;Dbxref=GenBank:WP_021204922.1;Name=WP_021204922.1;Ontology_term=GO:0033103;end_range=493,.;gbkey=CDS;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248954.1;locus_tag=DY927_RS00005;partial=true;product=Hcp family type VI secretion system effector;protein_id=WP_021204922.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY927_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY927_RS00010' for NZ_RXSY01000002.1 Protein Homology CDS 189 589 +
dbxref : GenBank:WP_133457607.1
end_range : 590,.
gbkey : CDS
id : cds-WP_133457607.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250202.1
locus_tag : DY927_RS00010
name : WP_133457607.1
parent : gene-DY927_RS00010
partial : true
product : contractile injection system protein%2C VgrG/Pvc8 family
protein_id : WP_133457607.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271841/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RXSY01000002.1 Protein Homology CDS 190 590 . + 0 ID=cds-WP_133457607.1;Parent=gene-DY927_RS00010;Dbxref=GenBank:WP_133457607.1;Name=WP_133457607.1;end_range=590,.;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250202.1;locus_tag=DY927_RS00010;partial=true;product=contractile injection system protein%2C VgrG/Pvc8 family;protein_id=WP_133457607.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY927_RS35365' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY927_RS35365' for NZ_RXSY01000003.1 GeneMarkS-2+ CDS 0 233 -
dbxref : GenBank:WP_205871273.1
gbkey : CDS
id : cds-WP_205871273.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY927_RS35365
name : WP_205871273.1
parent : gene-DY927_RS35365
partial : true
product : hypothetical protein
protein_id : WP_205 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271842/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271842/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271842/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271842/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271842/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY955_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY955_RS00005' for NZ_RXUA01000001.1 Protein Homology CDS 0 1161 +
dbxref : GenBank:WP_126571767.1
gbkey : CDS
gene : umuC
go_function : damaged DNA binding|0003684||IEA
go_process : DNA repair|0006281||IEA
id : cds-WP_126571767.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012053998.1
locus_tag : DY955_RS00005
name : WP_126571767.1
ontology_term : GO:0006281,GO:0003684
parent : gene-DY955_RS00005
partial : true
product : translesion error-prone DNA polymerase V subunit UmuC
protein_id : WP_126571767.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271842/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUA01000001.1 Protein Homology CDS 1 1162 . + 1 ID=cds-WP_126571767.1;Parent=gene-DY955_RS00005;Dbxref=GenBank:WP_126571767.1;Name=WP_126571767.1;Ontology_term=GO:0006281,GO:0003684;gbkey=CDS;gene=umuC;go_function=damaged DNA binding|0003684||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012053998.1;locus_tag=DY955_RS00005;partial=true;product=translesion error-prone DNA polymerase V subunit UmuC;protein_id=WP_126571767.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY955_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY955_RS00010' for NZ_RXUA01000001.1 GeneMarkS-2+ CDS 1220 2125 +
dbxref : GenBank:WP_124188772.1
gbkey : CDS
id : cds-WP_124188772.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY955_RS00010
name : WP_124188772.1
parent : gene-DY955_RS00010
product : hypothetical protein
protein_id : WP_124188772.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271842/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUA01000001.1 GeneMarkS-2+ CDS 1221 2126 . + 0 ID=cds-WP_124188772.1;Parent=gene-DY955_RS00010;Dbxref=GenBank:WP_124188772.1;Name=WP_124188772.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY955_RS00010;product=hypothetical protein;protein_id=WP_124188772.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY955_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY955_RS00015' for NZ_RXUA01000001.1 GeneMarkS-2+ CDS 2119 2382 +
dbxref : GenBank:WP_124188773.1
gbkey : CDS
id : cds-WP_124188773.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY955_RS00015
name : WP_124188773.1
parent : gene-DY955_RS00015
product : hypothetical protein
protein_id : WP_124188773.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271842/working/snpeff_output/Pseudo |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271843/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271843/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271843/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271843/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271843/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY954_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY954_RS00005' for NZ_RXTZ01000001.1 Protein Homology CDS 389 2320 +
dbxref : GenBank:WP_023113308.1
gbkey : CDS
gene : eatR
id : cds-WP_023113308.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252710.1
locus_tag : DY954_RS00005
name : WP_023113308.1
parent : gene-DY954_RS00005
product : sigma-54-dependent transcriptional regulator EatR
protein_id : WP_023113308.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271843/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTZ01000001.1 Protein Homology CDS 390 2321 . + 0 ID=cds-WP_023113308.1;Parent=gene-DY954_RS00005;Dbxref=GenBank:WP_023113308.1;Name=WP_023113308.1;gbkey=CDS;gene=eatR;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252710.1;locus_tag=DY954_RS00005;product=sigma-54-dependent transcriptional regulator EatR;protein_id=WP_023113308.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY954_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY954_RS00015' for NZ_RXTZ01000001.1 Protein Homology CDS 3843 4472 +
dbxref : GenBank:WP_003093227.1
gbkey : CDS
gene : ubiX
id : cds-WP_003093227.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252708.1
locus_tag : DY954_RS00015
name : WP_003093227.1
parent : gene-DY954_RS00015
product : flavin prenyltransferase UbiX
protein_id : WP_003093227.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271843/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTZ01000001.1 Protein Homology CDS 3844 4473 . + 0 ID=cds-WP_003093227.1;Parent=gene-DY954_RS00015;Dbxref=GenBank:WP_003093227.1;Name=WP_003093227.1;gbkey=CDS;gene=ubiX;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252708.1;locus_tag=DY954_RS00015;product=flavin prenyltransferase UbiX;protein_id=WP_003093227.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY954_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY954_RS00020' for NZ_RXTZ01000001.1 Protein Homology CDS 4501 4749 +
dbxref : GenBank:WP_042159398.1
gbkey : CDS
id : cds-WP_042159398.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003244079.1
locus_tag : DY954_RS00020
name : WP_042159398.1
parent : gene-DY954_RS00020
product : YceK/YidQ family lipoprotein
protein_id : WP_042159398.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271843/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXTZ01000001.1 Protein Homology CDS 4502 4750 . + 0 ID=cds-WP_042159398.1;Parent=gene-DY954_RS00020;Dbxref=GenBank:WP_042159398.1;Name=WP_042159398.1;gbkey=CDS;inference=COORDINATES: si |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271844/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271844/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271844/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271844/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271844/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY974_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY974_RS00010' for NZ_RXUT01000001.1 GeneMarkS-2+ CDS 491 3760 +
dbxref : GenBank:WP_124207080.1
gbkey : CDS
id : cds-WP_124207080.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY974_RS00010
name : WP_124207080.1
parent : gene-DY974_RS00010
product : hypothetical protein
protein_id : WP_124207080.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271844/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUT01000001.1 GeneMarkS-2+ CDS 492 3761 . + 0 ID=cds-WP_124207080.1;Parent=gene-DY974_RS00010;Dbxref=GenBank:WP_124207080.1;Name=WP_124207080.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY974_RS00010;product=hypothetical protein;protein_id=WP_124207080.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY974_RS30690' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY974_RS30690' for NZ_RXUT01000001.1 Protein Homology CDS 4339 4962 +
dbxref : GenBank:WP_003099240.1
gbkey : CDS
id : cds-WP_003099240.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003099240.1
locus_tag : DY974_RS30690
name : WP_003099240.1
parent : gene-DY974_RS30690
product : hypothetical protein
protein_id : WP_003099240.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271844/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUT01000001.1 Protein Homology CDS 4340 4963 . + 0 ID=cds-WP_003099240.1;Parent=gene-DY974_RS30690;Dbxref=GenBank:WP_003099240.1;Name=WP_003099240.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003099240.1;locus_tag=DY974_RS30690;product=hypothetical protein;protein_id=WP_003099240.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY974_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY974_RS00020' for NZ_RXUT01000001.1 Protein Homology CDS 5106 6500 -
dbxref : GenBank:WP_003114030.1
gbkey : CDS
gene : argH
go_function : argininosuccinate lyase activity|0004056||IEA
go_process : arginine biosynthetic process via ornithine|0042450||IEA
id : cds-WP_003114030.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253950.1
locus_tag : DY974_RS00020
name : WP_003114030.1
ontology_term : GO:0042450,GO:0004056
parent : gene-DY974_RS00020
product : argininosuccinate lyase
protein_id : WP_003114030.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271844/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RXUT01000001.1 Protein Homology CDS 5107 6501 . - 0 ID=cds-WP_003114030.1;Parent=gene-DY974_RS00020;Dbxref=GenBank:WP_003114030.1;Name=WP_003114030.1;Ontolo |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271845/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271845/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271845/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271845/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271845/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY967_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY967_RS00010' for NZ_RXUM01000001.1 Protein Homology CDS 4430 5401 +
dbxref : GenBank:WP_003146034.1
gbkey : CDS
go_function : oxidoreductase activity%2C acting on the CH-OH group of donors%2C NAD or NADP as acceptor|0016616||IEA,NAD binding|0051287||IEA
id : cds-WP_003146034.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253316.1
locus_tag : DY967_RS00010
name : WP_003146034.1
ontology_term : GO:0016616,GO:0051287
parent : gene-DY967_RS00010
product : 2-hydroxyacid dehydrogenase
protein_id : WP_003146034.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271845/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUM01000001.1 Protein Homology CDS 4431 5402 . + 0 ID=cds-WP_003146034.1;Parent=gene-DY967_RS00010;Dbxref=GenBank:WP_003146034.1;Name=WP_003146034.1;Ontology_term=GO:0016616,GO:0051287;gbkey=CDS;go_function=oxidoreductase activity%2C acting on the CH-OH group of donors%2C NAD or NADP as acceptor|0016616||IEA,NAD binding|0051287||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253316.1;locus_tag=DY967_RS00010;product=2-hydroxyacid dehydrogenase;protein_id=WP_003146034.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY967_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY967_RS00015' for NZ_RXUM01000001.1 Protein Homology CDS 5511 6509 +
dbxref : GenBank:WP_003117439.1
gbkey : CDS
go_function : methyltransferase activity|0008168||IEA
id : cds-WP_003117439.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253317.1
locus_tag : DY967_RS00015
name : WP_003117439.1
ontology_term : GO:0008168
parent : gene-DY967_RS00015
product : class I SAM-dependent methyltransferase
protein_id : WP_003117439.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271845/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUM01000001.1 Protein Homology CDS 5512 6510 . + 0 ID=cds-WP_003117439.1;Parent=gene-DY967_RS00015;Dbxref=GenBank:WP_003117439.1;Name=WP_003117439.1;Ontology_term=GO:0008168;gbkey=CDS;go_function=methyltransferase activity|0008168||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253317.1;locus_tag=DY967_RS00015;product=class I SAM-dependent methyltransferase;protein_id=WP_003117439.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY967_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY967_RS00020' for NZ_RXUM01000001.1 Protein Homology CDS 6604 8067 +
dbxref : GenBank:WP_023087815.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : amino acid transmembrane transporter activity|0015171||IEA
go_process : amino acid tra |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271846/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271846/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271846/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271846/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271846/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY978_RS32945' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY978_RS32945' for NZ_RXUY01000001.1 GeneMarkS-2+ CDS 0 388 +
dbxref : GenBank:WP_221768187.1
gbkey : CDS
id : cds-WP_221768187.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY978_RS32945
name : WP_221768187.1
parent : gene-DY978_RS32945
partial : true
product : hypothetical protein
protein_id : WP_221768187.1
source : GeneMarkS-2+
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271846/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUY01000001.1 GeneMarkS-2+ CDS 1 389 . + 2 ID=cds-WP_221768187.1;Parent=gene-DY978_RS32945;Dbxref=GenBank:WP_221768187.1;Name=WP_221768187.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY978_RS32945;partial=true;product=hypothetical protein;protein_id=WP_221768187.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY978_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY978_RS00005' for NZ_RXUY01000001.1 Protein Homology CDS 337 1653 -
dbxref : GenBank:WP_003121322.1
gbkey : CDS
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003121322.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254057.1
locus_tag : DY978_RS00005
name : WP_003121322.1
ontology_term : GO:0055085,GO:0022857
parent : gene-DY978_RS00005
product : MFS transporter
protein_id : WP_003121322.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271846/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUY01000001.1 Protein Homology CDS 338 1654 . - 0 ID=cds-WP_003121322.1;Parent=gene-DY978_RS00005;Dbxref=GenBank:WP_003121322.1;Name=WP_003121322.1;Ontology_term=GO:0055085,GO:0022857;gbkey=CDS;go_function=transmembrane transporter activity|0022857||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254057.1;locus_tag=DY978_RS00005;product=MFS transporter;protein_id=WP_003121322.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY978_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY978_RS00010' for NZ_RXUY01000001.1 Protein Homology CDS 1941 2345 +
dbxref : GenBank:WP_003096677.1
gbkey : CDS
go_function : fatty acyl-CoA hydrolase activity|0047617||IEA
id : cds-WP_003096677.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254058.1
locus_tag : DY978_RS00010
name : WP_003096677.1
ontology_term : GO:0047617
parent : gene-DY978_RS00010
product : acyl-CoA thioesterase
protein_id : WP_003096677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scr |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271847/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271847/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271847/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271847/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271847/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ67_RS15315' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ67_RS15315' for NZ_RHSK01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGJ67_RS15315
name : WP_003096779.1
parent : gene-EGJ67_RS15315
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271847/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSK01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGJ67_RS15315;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGJ67_RS15315;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ67_RS15320' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ67_RS15320' for NZ_RHSK01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_023084796.1
gbkey : CDS
id : cds-WP_023084796.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGJ67_RS15320
name : WP_023084796.1
parent : gene-EGJ67_RS15320
product : sarcosine oxidase subunit delta
protein_id : WP_023084796.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271847/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSK01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_023084796.1;Parent=gene-EGJ67_RS15320;Dbxref=GenBank:WP_023084796.1;Name=WP_023084796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGJ67_RS15320;product=sarcosine oxidase subunit delta;protein_id=WP_023084796.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ67_RS15325' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ67_RS15325' for NZ_RHSK01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003162069.1
gbkey : CDS
id : cds-WP_003162069.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGJ67_RS15325
name : WP_003162069.1
parent : gene-EGJ67_RS15325
product : sarcosine oxidase subunit alpha
protein_id : WP_003162069.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271847/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSK01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003162069.1;Parent=gene-EGJ67_RS15325;Dbxref=GenBank:WP_003162069.1;Name=WP_003162069.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGJ67_RS15325;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271848/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271848/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271848/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271848/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271848/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGK43_RS14925' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGK43_RS14925' for NZ_RHSE01000010.1 Protein Homology CDS 0 327 +
dbxref : GenBank:WP_044727449.1
gbkey : CDS
go_process : DNA integration|0015074||IEA
id : cds-WP_044727449.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_086558210.1
locus_tag : EGK43_RS14925
name : WP_044727449.1
ontology_term : GO:0015074
parent : gene-EGK43_RS14925
partial : true
product : integrase core domain-containing protein
protein_id : WP_044727449.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271848/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSE01000010.1 Protein Homology CDS 1 328 . + 1 ID=cds-WP_044727449.1;Parent=gene-EGK43_RS14925;Dbxref=GenBank:WP_044727449.1;Name=WP_044727449.1;Ontology_term=GO:0015074;gbkey=CDS;go_process=DNA integration|0015074||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_086558210.1;locus_tag=EGK43_RS14925;partial=true;product=integrase core domain-containing protein;protein_id=WP_044727449.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGK43_RS14935' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGK43_RS14935' for NZ_RHSE01000010.1 Protein Homology CDS 1043 1399 -
dbxref : GenBank:WP_003090655.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA
id : cds-WP_003090655.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251427.2
locus_tag : EGK43_RS14935
name : WP_003090655.1
ontology_term : GO:0003677,GO:0003700
parent : gene-EGK43_RS14935
product : MerR family transcriptional regulator
protein_id : WP_003090655.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271848/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_RHSE01000010.1 Protein Homology CDS 1044 1400 . - 0 ID=cds-WP_003090655.1;Parent=gene-EGK43_RS14935;Dbxref=GenBank:WP_003090655.1;Name=WP_003090655.1;Ontology_term=GO:0003677,GO:0003700;gbkey=CDS;go_function=DNA binding|0003677||IEA,DNA-binding transcription factor activity|0003700||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251427.2;locus_tag=EGK43_RS14935;product=MerR family transcriptional regulator;protein_id=WP_003090655.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGK43_RS14940' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGK43_RS14940' for NZ_RHSE01000010.1 Protein Homology CDS 1380 1682 -
dbxref : GenBank:WP_003090661.1
gbkey : CDS
gene : ihfA
go_function : DNA binding|0003677||IEA
go_process : DNA recombination|0006310||IEA,regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_003090661.1
inferenc |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271849/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271849/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271849/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271849/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271849/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ83_RS30445' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ83_RS30445' for NZ_RHSA01000100.1 Protein Homology CDS 179 1471 +
dbxref : GenBank:WP_125488221.1
gbkey : CDS
id : cds-WP_125488221.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249418.1
locus_tag : EGJ83_RS30445
name : WP_125488221.1
parent : gene-EGJ83_RS30445
product : hypothetical protein
protein_id : WP_125488221.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271849/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSA01000100.1 Protein Homology CDS 180 1472 . + 0 ID=cds-WP_125488221.1;Parent=gene-EGJ83_RS30445;Dbxref=GenBank:WP_125488221.1;Name=WP_125488221.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249418.1;locus_tag=EGJ83_RS30445;product=hypothetical protein;protein_id=WP_125488221.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ83_RS30450' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ83_RS30450' for NZ_RHSA01000100.1 Protein Homology CDS 1471 2454 +
dbxref : GenBank:WP_033942044.1
gbkey : CDS
go_function : DNA binding|0003677||IEA
go_process : DNA recombination|0006310||IEA,DNA integration|0015074||IEA
id : cds-WP_033942044.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249419.1
locus_tag : EGJ83_RS30450
name : WP_033942044.1
ontology_term : GO:0006310,GO:0015074,GO:0003677
parent : gene-EGJ83_RS30450
product : tyrosine-type recombinase/integrase
protein_id : WP_033942044.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271849/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSA01000100.1 Protein Homology CDS 1472 2455 . + 0 ID=cds-WP_033942044.1;Parent=gene-EGJ83_RS30450;Dbxref=GenBank:WP_033942044.1;Name=WP_033942044.1;Ontology_term=GO:0006310,GO:0015074,GO:0003677;gbkey=CDS;go_function=DNA binding|0003677||IEA;go_process=DNA recombination|0006310||IEA,DNA integration|0015074||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249419.1;locus_tag=EGJ83_RS30450;product=tyrosine-type recombinase/integrase;protein_id=WP_033942044.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ83_RS30455' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ83_RS30455' for NZ_RHSA01000100.1 Protein Homology CDS 2668 2919 +
dbxref : GenBank:WP_003114155.1
gbkey : CDS
id : cds-WP_003114155.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003114155.1
locus_tag : EGJ83_RS30455
name : WP_003114155.1
parent : gene-EGJ83_RS30455
product : type II toxin-antitoxin system Phd/YefM family antitoxin
protein_id : WP_003114155.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/7227 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271850/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271850/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271850/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271850/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271850/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ74_RS15725' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ74_RS15725' for NZ_RHSD01000010.1 Protein Homology CDS 252 2030 -
dbxref : GenBank:WP_003103344.1
gbkey : CDS
id : cds-WP_003103344.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249199.1
locus_tag : EGJ74_RS15725
name : WP_003103344.1
parent : gene-EGJ74_RS15725
product : acyl-CoA dehydrogenase C-terminal domain-containing protein
protein_id : WP_003103344.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271850/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSD01000010.1 Protein Homology CDS 253 2031 . - 0 ID=cds-WP_003103344.1;Parent=gene-EGJ74_RS15725;Dbxref=GenBank:WP_003103344.1;Name=WP_003103344.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249199.1;locus_tag=EGJ74_RS15725;product=acyl-CoA dehydrogenase C-terminal domain-containing protein;protein_id=WP_003103344.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ74_RS15735' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ74_RS15735' for NZ_RHSD01000010.1 Protein Homology CDS 2303 4099 -
dbxref : GenBank:WP_003160871.1
gbkey : CDS
id : cds-WP_003160871.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249198.1
locus_tag : EGJ74_RS15735
name : WP_003160871.1
parent : gene-EGJ74_RS15735
product : acyl-CoA dehydrogenase C-terminal domain-containing protein
protein_id : WP_003160871.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271850/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSD01000010.1 Protein Homology CDS 2304 4100 . - 0 ID=cds-WP_003160871.1;Parent=gene-EGJ74_RS15735;Dbxref=GenBank:WP_003160871.1;Name=WP_003160871.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249198.1;locus_tag=EGJ74_RS15735;product=acyl-CoA dehydrogenase C-terminal domain-containing protein;protein_id=WP_003160871.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ74_RS15740' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ74_RS15740' for NZ_RHSD01000010.1 Protein Homology CDS 4312 6117 -
dbxref : GenBank:WP_003084842.1
gbkey : CDS
id : cds-WP_003084842.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249197.1
locus_tag : EGJ74_RS15740
name : WP_003084842.1
parent : gene-EGJ74_RS15740
product : phenylacyl-CoA dehydrogenase
protein_id : WP_003084842.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271850/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSD01000010.1 Protein Homology CDS 4313 6118 . - 0 ID=cds-WP_003084842.1;Parent=gene-EGJ74_RS15740;Dbxref=GenBank:WP_003084842.1;Name=WP_003084842.1;gbke |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271851/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271851/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271851/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271851/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271851/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ81_RS18490' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ81_RS18490' for NZ_RHSS01000010.1 Protein Homology CDS 0 1286 -
dbxref : GenBank:WP_074198678.1
gbkey : CDS
gene : nuoL
go_function : NADH dehydrogenase (ubiquinone) activity|0008137||IEA
go_process : ATP synthesis coupled electron transport|0042773||IEA
id : cds-WP_074198678.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251337.1
locus_tag : EGJ81_RS18490
name : WP_074198678.1
ontology_term : GO:0042773,GO:0008137
parent : gene-EGJ81_RS18490
partial : true
product : NADH-quinone oxidoreductase subunit L
protein_id : WP_074198678.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271851/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSS01000010.1 Protein Homology CDS 1 1287 . - 0 ID=cds-WP_074198678.1;Parent=gene-EGJ81_RS18490;Dbxref=GenBank:WP_074198678.1;Name=WP_074198678.1;Ontology_term=GO:0042773,GO:0008137;gbkey=CDS;gene=nuoL;go_function=NADH dehydrogenase (ubiquinone) activity|0008137||IEA;go_process=ATP synthesis coupled electron transport|0042773||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251337.1;locus_tag=EGJ81_RS18490;partial=true;product=NADH-quinone oxidoreductase subunit L;protein_id=WP_074198678.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ81_RS18495' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ81_RS18495' for NZ_RHSS01000010.1 Protein Homology CDS 1283 1591 -
dbxref : GenBank:WP_003090475.1
gbkey : CDS
gene : nuoK
go_function : oxidoreductase activity%2C acting on NAD(P)H|0016651||IEA
go_process : ATP synthesis coupled electron transport|0042773||IEA
id : cds-WP_003090475.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251336.1
locus_tag : EGJ81_RS18495
name : WP_003090475.1
ontology_term : GO:0042773,GO:0016651
parent : gene-EGJ81_RS18495
product : NADH-quinone oxidoreductase subunit NuoK
protein_id : WP_003090475.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271851/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSS01000010.1 Protein Homology CDS 1284 1592 . - 0 ID=cds-WP_003090475.1;Parent=gene-EGJ81_RS18495;Dbxref=GenBank:WP_003090475.1;Name=WP_003090475.1;Ontology_term=GO:0042773,GO:0016651;gbkey=CDS;gene=nuoK;go_function=oxidoreductase activity%2C acting on NAD(P)H|0016651||IEA;go_process=ATP synthesis coupled electron transport|0042773||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251336.1;locus_tag=EGJ81_RS18495;product=NADH-quinone oxidoreductase subunit NuoK;protein_id=WP_003090475.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ81_RS18500' is a Gene instead of a transcri |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271852/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271852/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271852/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271852/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271852/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ70_RS15620' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ70_RS15620' for NZ_RHSP01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGJ70_RS15620
name : WP_003096779.1
parent : gene-EGJ70_RS15620
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271852/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSP01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGJ70_RS15620;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGJ70_RS15620;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ70_RS15625' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ70_RS15625' for NZ_RHSP01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_023084796.1
gbkey : CDS
id : cds-WP_023084796.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGJ70_RS15625
name : WP_023084796.1
parent : gene-EGJ70_RS15625
product : sarcosine oxidase subunit delta
protein_id : WP_023084796.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271852/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSP01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_023084796.1;Parent=gene-EGJ70_RS15625;Dbxref=GenBank:WP_023084796.1;Name=WP_023084796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGJ70_RS15625;product=sarcosine oxidase subunit delta;protein_id=WP_023084796.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ70_RS15630' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ70_RS15630' for NZ_RHSP01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003162069.1
gbkey : CDS
id : cds-WP_003162069.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGJ70_RS15630
name : WP_003162069.1
parent : gene-EGJ70_RS15630
product : sarcosine oxidase subunit alpha
protein_id : WP_003162069.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271852/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSP01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003162069.1;Parent=gene-EGJ70_RS15630;Dbxref=GenBank:WP_003162069.1;Name=WP_003162069.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGJ70_RS15630;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271853/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271853/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271853/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271853/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271853/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ59_RS19830' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ59_RS19830' for NZ_RHSJ01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGJ59_RS19830
name : WP_003096779.1
parent : gene-EGJ59_RS19830
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271853/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSJ01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGJ59_RS19830;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGJ59_RS19830;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ59_RS19835' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ59_RS19835' for NZ_RHSJ01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_003096781.1
gbkey : CDS
id : cds-WP_003096781.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGJ59_RS19835
name : WP_003096781.1
parent : gene-EGJ59_RS19835
product : sarcosine oxidase subunit delta
protein_id : WP_003096781.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271853/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSJ01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_003096781.1;Parent=gene-EGJ59_RS19835;Dbxref=GenBank:WP_003096781.1;Name=WP_003096781.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGJ59_RS19835;product=sarcosine oxidase subunit delta;protein_id=WP_003096781.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ59_RS19840' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ59_RS19840' for NZ_RHSJ01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003117184.1
gbkey : CDS
id : cds-WP_003117184.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGJ59_RS19840
name : WP_003117184.1
parent : gene-EGJ59_RS19840
product : sarcosine oxidase subunit alpha
protein_id : WP_003117184.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271853/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSJ01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003117184.1;Parent=gene-EGJ59_RS19840;Dbxref=GenBank:WP_003117184.1;Name=WP_003117184.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGJ59_RS19840;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271854/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271854/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271854/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271854/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271854/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ76_RS15315' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ76_RS15315' for NZ_RHST01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGJ76_RS15315
name : WP_003096779.1
parent : gene-EGJ76_RS15315
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271854/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHST01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGJ76_RS15315;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGJ76_RS15315;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ76_RS15320' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ76_RS15320' for NZ_RHST01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_023084796.1
gbkey : CDS
id : cds-WP_023084796.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGJ76_RS15320
name : WP_023084796.1
parent : gene-EGJ76_RS15320
product : sarcosine oxidase subunit delta
protein_id : WP_023084796.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271854/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHST01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_023084796.1;Parent=gene-EGJ76_RS15320;Dbxref=GenBank:WP_023084796.1;Name=WP_023084796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGJ76_RS15320;product=sarcosine oxidase subunit delta;protein_id=WP_023084796.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ76_RS15325' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ76_RS15325' for NZ_RHST01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003162069.1
gbkey : CDS
id : cds-WP_003162069.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGJ76_RS15325
name : WP_003162069.1
parent : gene-EGJ76_RS15325
product : sarcosine oxidase subunit alpha
protein_id : WP_003162069.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271854/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHST01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003162069.1;Parent=gene-EGJ76_RS15325;Dbxref=GenBank:WP_003162069.1;Name=WP_003162069.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGJ76_RS15325;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271855/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271855/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271855/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271855/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271855/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ66_RS14210' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ66_RS14210' for NZ_RHSQ01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGJ66_RS14210
name : WP_003096779.1
parent : gene-EGJ66_RS14210
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271855/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSQ01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGJ66_RS14210;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGJ66_RS14210;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ66_RS14215' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ66_RS14215' for NZ_RHSQ01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_023084796.1
gbkey : CDS
id : cds-WP_023084796.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGJ66_RS14215
name : WP_023084796.1
parent : gene-EGJ66_RS14215
product : sarcosine oxidase subunit delta
protein_id : WP_023084796.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271855/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSQ01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_023084796.1;Parent=gene-EGJ66_RS14215;Dbxref=GenBank:WP_023084796.1;Name=WP_023084796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGJ66_RS14215;product=sarcosine oxidase subunit delta;protein_id=WP_023084796.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ66_RS14220' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ66_RS14220' for NZ_RHSQ01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003162069.1
gbkey : CDS
id : cds-WP_003162069.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGJ66_RS14220
name : WP_003162069.1
parent : gene-EGJ66_RS14220
product : sarcosine oxidase subunit alpha
protein_id : WP_003162069.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271855/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSQ01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003162069.1;Parent=gene-EGJ66_RS14220;Dbxref=GenBank:WP_003162069.1;Name=WP_003162069.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGJ66_RS14220;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271856/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271856/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271856/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271856/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271856/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGP97_RS19635' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGP97_RS19635' for NZ_RHSN01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGP97_RS19635
name : WP_003096779.1
parent : gene-EGP97_RS19635
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271856/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSN01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGP97_RS19635;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGP97_RS19635;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGP97_RS19640' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGP97_RS19640' for NZ_RHSN01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_003096781.1
gbkey : CDS
id : cds-WP_003096781.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGP97_RS19640
name : WP_003096781.1
parent : gene-EGP97_RS19640
product : sarcosine oxidase subunit delta
protein_id : WP_003096781.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271856/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSN01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_003096781.1;Parent=gene-EGP97_RS19640;Dbxref=GenBank:WP_003096781.1;Name=WP_003096781.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGP97_RS19640;product=sarcosine oxidase subunit delta;protein_id=WP_003096781.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGP97_RS19645' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGP97_RS19645' for NZ_RHSN01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003117184.1
gbkey : CDS
id : cds-WP_003117184.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGP97_RS19645
name : WP_003117184.1
parent : gene-EGP97_RS19645
product : sarcosine oxidase subunit alpha
protein_id : WP_003117184.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271856/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSN01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003117184.1;Parent=gene-EGP97_RS19645;Dbxref=GenBank:WP_003117184.1;Name=WP_003117184.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGP97_RS19645;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271857/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271857/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271857/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271857/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271857/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ63_RS15510' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ63_RS15510' for NZ_RHSR01000010.1 Protein Homology CDS 540 1910 +
dbxref : GenBank:WP_003106497.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
id : cds-WP_003106497.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250731.1
locus_tag : EGJ63_RS15510
name : WP_003106497.1
ontology_term : GO:0022857,GO:0016020
parent : gene-EGJ63_RS15510
product : APC family permease
protein_id : WP_003106497.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271857/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSR01000010.1 Protein Homology CDS 541 1911 . + 0 ID=cds-WP_003106497.1;Parent=gene-EGJ63_RS15510;Dbxref=GenBank:WP_003106497.1;Name=WP_003106497.1;Ontology_term=GO:0022857,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=transmembrane transporter activity|0022857||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250731.1;locus_tag=EGJ63_RS15510;product=APC family permease;protein_id=WP_003106497.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ63_RS15520' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ63_RS15520' for NZ_RHSR01000010.1 Protein Homology CDS 2398 3627 +
dbxref : GenBank:WP_003106499.1
gbkey : CDS
gene : sstT
go_component : membrane|0016020||IEA
go_function : symporter activity|0015293||IEA
go_process : threonine transport|0015826||IEA,serine transport|0032329||IEA
id : cds-WP_003106499.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250732.1
locus_tag : EGJ63_RS15520
name : WP_003106499.1
ontology_term : GO:0015826,GO:0032329,GO:0015293,GO:0016020
parent : gene-EGJ63_RS15520
product : serine/threonine transporter SstT
protein_id : WP_003106499.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271857/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSR01000010.1 Protein Homology CDS 2399 3628 . + 0 ID=cds-WP_003106499.1;Parent=gene-EGJ63_RS15520;Dbxref=GenBank:WP_003106499.1;Name=WP_003106499.1;Ontology_term=GO:0015826,GO:0032329,GO:0015293,GO:0016020;gbkey=CDS;gene=sstT;go_component=membrane|0016020||IEA;go_function=symporter activity|0015293||IEA;go_process=threonine transport|0015826||IEA,serine transport|0032329||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250732.1;locus_tag=EGJ63_RS15520;product=serine/threonine transporter SstT;protein_id=WP_003106499.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ63_RS15525' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ63_RS15525' for NZ_RHSR01000010.1 Protein Homology CDS 3748 4650 +
dbxref : GenBank:WP_003114880.1 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271858/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271858/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271858/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271858/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271858/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGQ15_RS20055' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGQ15_RS20055' for NZ_RHSM01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGQ15_RS20055
name : WP_003096779.1
parent : gene-EGQ15_RS20055
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271858/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSM01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGQ15_RS20055;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGQ15_RS20055;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGQ15_RS20060' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGQ15_RS20060' for NZ_RHSM01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_003096781.1
gbkey : CDS
id : cds-WP_003096781.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGQ15_RS20060
name : WP_003096781.1
parent : gene-EGQ15_RS20060
product : sarcosine oxidase subunit delta
protein_id : WP_003096781.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271858/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSM01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_003096781.1;Parent=gene-EGQ15_RS20060;Dbxref=GenBank:WP_003096781.1;Name=WP_003096781.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGQ15_RS20060;product=sarcosine oxidase subunit delta;protein_id=WP_003096781.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGQ15_RS20065' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGQ15_RS20065' for NZ_RHSM01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003117184.1
gbkey : CDS
id : cds-WP_003117184.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGQ15_RS20065
name : WP_003117184.1
parent : gene-EGQ15_RS20065
product : sarcosine oxidase subunit alpha
protein_id : WP_003117184.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271858/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSM01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003117184.1;Parent=gene-EGQ15_RS20065;Dbxref=GenBank:WP_003117184.1;Name=WP_003117184.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGQ15_RS20065;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271859/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271859/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271859/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271859/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271859/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGQ13_RS30840' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGQ13_RS30840' for NZ_RHSO01000010.1 Protein Homology CDS 0 107 +
dbxref : GenBank:WP_234499630.1
gbkey : CDS
id : cds-WP_234499630.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250674.1
locus_tag : EGQ13_RS30840
name : WP_234499630.1
parent : gene-EGQ13_RS30840
partial : true
product : hypothetical protein
protein_id : WP_234499630.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271859/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSO01000010.1 Protein Homology CDS 1 108 . + 0 ID=cds-WP_234499630.1;Parent=gene-EGQ13_RS30840;Dbxref=GenBank:WP_234499630.1;Name=WP_234499630.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250674.1;locus_tag=EGQ13_RS30840;partial=true;product=hypothetical protein;protein_id=WP_234499630.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGQ13_RS15345' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGQ13_RS15345' for NZ_RHSO01000010.1 Protein Homology CDS 317 1765 +
dbxref : GenBank:WP_003093230.1
gbkey : CDS
gene : eat
go_component : membrane|0016020||IEA
go_function : amino acid transmembrane transporter activity|0015171||IEA
go_process : amino acid transport|0006865||IEA
id : cds-WP_003093230.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252712.1
locus_tag : EGQ13_RS15345
name : WP_003093230.1
ontology_term : GO:0006865,GO:0015171,GO:0016020
parent : gene-EGQ13_RS15345
product : ethanolamine permease
protein_id : WP_003093230.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271859/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSO01000010.1 Protein Homology CDS 318 1766 . + 0 ID=cds-WP_003093230.1;Parent=gene-EGQ13_RS15345;Dbxref=GenBank:WP_003093230.1;Name=WP_003093230.1;Ontology_term=GO:0006865,GO:0015171,GO:0016020;gbkey=CDS;gene=eat;go_component=membrane|0016020||IEA;go_function=amino acid transmembrane transporter activity|0015171||IEA;go_process=amino acid transport|0006865||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252712.1;locus_tag=EGQ13_RS15345;product=ethanolamine permease;protein_id=WP_003093230.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGQ13_RS15350' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGQ13_RS15350' for NZ_RHSO01000010.1 Protein Homology CDS 1823 3217 +
dbxref : GenBank:WP_003093232.1
gbkey : CDS
id : cds-WP_003093232.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252713.1
locus_tag : EGQ13_RS15350
name : WP_003093232.1
parent : gene-EGQ13_RS15350
product : ethanolamine ammonia-lyase subunit EutB
protein_id |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271860/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271860/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271860/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271860/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271860/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM443_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM443_RS00005' for NZ_MPBU01000001.1 Protein Homology CDS 482 2026 +
dbxref : GenBank:WP_003109151.1
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003109151.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064721.1
locus_tag : AM443_RS00005
name : WP_003109151.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-AM443_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003109151.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271860/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_MPBU01000001.1 Protein Homology CDS 483 2027 . + 0 ID=cds-WP_003109151.1;Parent=gene-AM443_RS00005;Dbxref=GenBank:WP_003109151.1;Name=WP_003109151.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_064721.1;locus_tag=AM443_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003109151.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM443_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM443_RS00010' for NZ_MPBU01000001.1 Protein Homology CDS 2055 3158 +
dbxref : GenBank:WP_019725660.1
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_019725660.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064722.1
locus_tag : AM443_RS00010
name : WP_019725660.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-AM443_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_019725660.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271860/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_MPBU01000001.1 Protein Homology CDS 2056 3159 . + 0 ID=cds-WP_019725660.1;Parent=gene-AM443_RS00010;Dbxref=GenBank:WP_019725660.1;Name=WP_019725660.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||I |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271861/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271861/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271861/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271861/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271861/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB97_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB97_RS00005' for NZ_CP027165.1 Protein Homology CDS 0 1580 +
dbxref : GenBank:WP_003162594.1
gbkey : CDS
id : cds-WP_003162594.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252514.1
locus_tag : CSB97_RS00005
name : WP_003162594.1
parent : gene-CSB97_RS00005
product : EAL domain-containing protein
protein_id : WP_003162594.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271861/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP027165.1 Protein Homology CDS 1 1581 . + 0 ID=cds-WP_003162594.1;Parent=gene-CSB97_RS00005;Dbxref=GenBank:WP_003162594.1;Name=WP_003162594.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252514.1;locus_tag=CSB97_RS00005;product=EAL domain-containing protein;protein_id=WP_003162594.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB97_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB97_RS00015' for NZ_CP027165.1 Protein Homology CDS 3071 3254 -
dbxref : GenBank:WP_223656237.1
exception : ribosomal slippage
gbkey : CDS
go_function : transposase activity|0004803||IEA
id : cds-WP_223656237.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_076611949.1
locus_tag : CSB97_RS00015
name : WP_223656237.1
note : programmed frameshift
ontology_term : GO:0004803
parent : gene-CSB97_RS00015
product : IS3 family transposase
protein_id : WP_223656237.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271861/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP027165.1 Protein Homology CDS 3072 3255 . - 0 ID=cds-WP_223656237.1;Parent=gene-CSB97_RS00015;Dbxref=GenBank:WP_223656237.1;Name=WP_223656237.1;Note=programmed frameshift;Ontology_term=GO:0004803;exception=ribosomal slippage;gbkey=CDS;go_function=transposase activity|0004803||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_076611949.1;locus_tag=CSB97_RS00015;product=IS3 family transposase;protein_id=WP_223656237.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB97_RS30610' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB97_RS30610' for NZ_CP027165.1 Protein Homology CDS 3730 4734 +
dbxref : GenBank:WP_023082206.1
gbkey : CDS
id : cds-WP_023082206.1
inference : COORDINATES: protein motif:HMM:NF037028.6
locus_tag : CSB97_RS30610
name : WP_023082206.1
parent : gene-CSB97_RS30610
product : lectin MOA-related protein
protein_id : WP_023082206.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271861/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_CP027165.1 Protein Homology CDS 3731 4735 . + 0 ID |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271862/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271862/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271862/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271862/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271862/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB93_RS01405' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB93_RS01405' for NZ_CP027169.1 Protein Homology CDS 150 878 -
dbxref : GenBank:WP_034081438.1
gbkey : CDS
gene : pgeF
id : cds-WP_034081438.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012077304.1
locus_tag : CSB93_RS01405
name : WP_034081438.1
parent : gene-CSB93_RS01405
product : peptidoglycan editing factor PgeF
protein_id : WP_034081438.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271862/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP027169.1 Protein Homology CDS 151 879 . - 0 ID=cds-WP_034081438.1;Parent=gene-CSB93_RS01405;Dbxref=GenBank:WP_034081438.1;Name=WP_034081438.1;gbkey=CDS;gene=pgeF;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012077304.1;locus_tag=CSB93_RS01405;product=peptidoglycan editing factor PgeF;protein_id=WP_034081438.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB93_RS01410' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB93_RS01410' for NZ_CP027169.1 Protein Homology CDS 875 1837 -
dbxref : GenBank:WP_003150035.1
gbkey : CDS
gene : rluD
go_function : RNA binding|0003723||IEA,pseudouridine synthase activity|0009982||IEA
go_process : pseudouridine synthesis|0001522||IEA,RNA modification|0009451||IEA
id : cds-WP_003150035.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253234.1
locus_tag : CSB93_RS01410
name : WP_003150035.1
ontology_term : GO:0001522,GO:0009451,GO:0003723,GO:0009982
parent : gene-CSB93_RS01410
product : 23S rRNA pseudouridine(1911/1915/1917) synthase RluD
protein_id : WP_003150035.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271862/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP027169.1 Protein Homology CDS 876 1838 . - 0 ID=cds-WP_003150035.1;Parent=gene-CSB93_RS01410;Dbxref=GenBank:WP_003150035.1;Name=WP_003150035.1;Ontology_term=GO:0001522,GO:0009451,GO:0003723,GO:0009982;gbkey=CDS;gene=rluD;go_function=RNA binding|0003723||IEA,pseudouridine synthase activity|0009982||IEA;go_process=pseudouridine synthesis|0001522||IEA,RNA modification|0009451||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253234.1;locus_tag=CSB93_RS01410;product=23S rRNA pseudouridine(1911/1915/1917) synthase RluD;protein_id=WP_003150035.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB93_RS01415' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB93_RS01415' for NZ_CP027169.1 Protein Homology CDS 1983 3008 +
dbxref : GenBank:WP_012077305.1
gbkey : CDS
id : cds-WP_012077305.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253235.1
locus_tag : CSB93_RS01415
name : WP_012077305.1
parent : gene-C |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271863/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271863/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271863/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271863/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271863/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB91_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB91_RS00005' for NZ_CP027171.1 Protein Homology CDS 0 1208 +
dbxref : GenBank:WP_003091258.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : ammonium channel activity|0008519||IEA
go_process : ammonium transmembrane transport|0072488||IEA
id : cds-WP_003091258.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009313807.1
locus_tag : CSB91_RS00005
name : WP_003091258.1
ontology_term : GO:0072488,GO:0008519,GO:0016020
parent : gene-CSB91_RS00005
product : ammonium transporter
protein_id : WP_003091258.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271863/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP027171.1 Protein Homology CDS 1 1209 . + 0 ID=cds-WP_003091258.1;Parent=gene-CSB91_RS00005;Dbxref=GenBank:WP_003091258.1;Name=WP_003091258.1;Ontology_term=GO:0072488,GO:0008519,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=ammonium channel activity|0008519||IEA;go_process=ammonium transmembrane transport|0072488||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009313807.1;locus_tag=CSB91_RS00005;product=ammonium transporter;protein_id=WP_003091258.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB91_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB91_RS00010' for NZ_CP027171.1 Protein Homology CDS 1393 2658 -
dbxref : GenBank:WP_003091257.1
gbkey : CDS
gene : opdQ
id : cds-WP_003091257.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251728.1
locus_tag : CSB91_RS00010
name : WP_003091257.1
parent : gene-CSB91_RS00010
product : porin OpdQ
protein_id : WP_003091257.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271863/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP027171.1 Protein Homology CDS 1394 2659 . - 0 ID=cds-WP_003091257.1;Parent=gene-CSB91_RS00010;Dbxref=GenBank:WP_003091257.1;Name=WP_003091257.1;gbkey=CDS;gene=opdQ;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251728.1;locus_tag=CSB91_RS00010;product=porin OpdQ;protein_id=WP_003091257.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB91_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB91_RS00015' for NZ_CP027171.1 Protein Homology CDS 2827 3693 -
dbxref : GenBank:WP_003091254.1
gbkey : CDS
go_function : hydrolase activity|0016787||IEA,metal ion binding|0046872||IEA
id : cds-WP_003091254.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251727.1
locus_tag : CSB91_RS00015
name : WP_003091254.1
ontology_term : GO:0016787,GO:0046872
parent : gene-CSB91_RS00015
product : MBL fold metallo-hydrolase
protein_id : WP_ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271864/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271864/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271864/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271864/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271864/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB85_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB85_RS00005' for NZ_CP027174.1 Protein Homology CDS 2 925 +
dbxref : GenBank:WP_003122138.1
gbkey : CDS
go_function : ATP binding|0005524||IEA,ATP hydrolysis activity|0016887||IEA,ABC-type transporter activity|0140359||IEA
id : cds-WP_003122138.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252362.1
locus_tag : CSB85_RS00005
name : WP_003122138.1
ontology_term : GO:0005524,GO:0016887,GO:0140359
parent : gene-CSB85_RS00005
product : ABC transporter ATP-binding protein
protein_id : WP_003122138.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271864/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP027174.1 Protein Homology CDS 3 926 . + 0 ID=cds-WP_003122138.1;Parent=gene-CSB85_RS00005;Dbxref=GenBank:WP_003122138.1;Name=WP_003122138.1;Ontology_term=GO:0005524,GO:0016887,GO:0140359;gbkey=CDS;go_function=ATP binding|0005524||IEA,ATP hydrolysis activity|0016887||IEA,ABC-type transporter activity|0140359||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252362.1;locus_tag=CSB85_RS00005;product=ABC transporter ATP-binding protein;protein_id=WP_003122138.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB85_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB85_RS00010' for NZ_CP027174.1 Protein Homology CDS 922 1656 +
dbxref : GenBank:WP_003117479.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : ATPase-coupled transmembrane transporter activity|0042626||IEA,ABC-type transporter activity|0140359||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003117479.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252361.1
locus_tag : CSB85_RS00010
name : WP_003117479.1
ontology_term : GO:0055085,GO:0042626,GO:0140359,GO:0016020
parent : gene-CSB85_RS00010
product : ABC transporter permease
protein_id : WP_003117479.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271864/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP027174.1 Protein Homology CDS 923 1657 . + 0 ID=cds-WP_003117479.1;Parent=gene-CSB85_RS00010;Dbxref=GenBank:WP_003117479.1;Name=WP_003117479.1;Ontology_term=GO:0055085,GO:0042626,GO:0140359,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=ATPase-coupled transmembrane transporter activity|0042626||IEA,ABC-type transporter activity|0140359||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252361.1;locus_tag=CSB85_RS00010;product=ABC transporter permease;protein_id=WP_003117479.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB85_RS00015' is a Gene instead of a transcript. Created |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271865/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271865/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271865/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271865/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271865/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB90_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB90_RS00005' for NZ_CP027172.1 Protein Homology CDS 2 490 -
dbxref : GenBank:WP_003083670.1
gbkey : CDS
gene : hcp
id : cds-WP_003083670.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248775.1
locus_tag : CSB90_RS00005
name : WP_003083670.1
parent : gene-CSB90_RS00005
product : type VI secretion system receptor/chaperone Hcp
protein_id : WP_003083670.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271865/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP027172.1 Protein Homology CDS 3 491 . - 0 ID=cds-WP_003083670.1;Parent=gene-CSB90_RS00005;Dbxref=GenBank:WP_003083670.1;Name=WP_003083670.1;gbkey=CDS;gene=hcp;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248775.1;locus_tag=CSB90_RS00005;product=type VI secretion system receptor/chaperone Hcp;protein_id=WP_003083670.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB90_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB90_RS00010' for NZ_CP027172.1 Protein Homology CDS 566 2062 -
dbxref : GenBank:WP_003104973.1
gbkey : CDS
gene : tssC
go_component : type VI protein secretion system complex|0033104||IEA
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_003104973.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248774.1
locus_tag : CSB90_RS00010
name : WP_003104973.1
ontology_term : GO:0033103,GO:0033104
parent : gene-CSB90_RS00010
product : type VI secretion system contractile sheath large subunit
protein_id : WP_003104973.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271865/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP027172.1 Protein Homology CDS 567 2063 . - 0 ID=cds-WP_003104973.1;Parent=gene-CSB90_RS00010;Dbxref=GenBank:WP_003104973.1;Name=WP_003104973.1;Ontology_term=GO:0033103,GO:0033104;gbkey=CDS;gene=tssC;go_component=type VI protein secretion system complex|0033104||IEA;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248774.1;locus_tag=CSB90_RS00010;product=type VI secretion system contractile sheath large subunit;protein_id=WP_003104973.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB90_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB90_RS00015' for NZ_CP027172.1 Protein Homology CDS 2075 2593 -
dbxref : GenBank:WP_003083666.1
gbkey : CDS
gene : tssB
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_003083666.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248773.1
lo |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271866/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271866/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271866/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271866/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271866/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB94_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB94_RS00005' for NZ_CP027166.1 Protein Homology CDS 3 1076 -
dbxref : GenBank:WP_003092054.1
gbkey : CDS
id : cds-WP_003092054.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252205.1
locus_tag : CSB94_RS00005
name : WP_003092054.1
parent : gene-CSB94_RS00005
product : class I SAM-dependent methyltransferase
protein_id : WP_003092054.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271866/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP027166.1 Protein Homology CDS 4 1077 . - 0 ID=cds-WP_003092054.1;Parent=gene-CSB94_RS00005;Dbxref=GenBank:WP_003092054.1;Name=WP_003092054.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252205.1;locus_tag=CSB94_RS00005;product=class I SAM-dependent methyltransferase;protein_id=WP_003092054.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB94_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB94_RS00010' for NZ_CP027166.1 Protein Homology CDS 1126 2577 -
dbxref : GenBank:WP_003092055.1
gbkey : CDS
id : cds-WP_003092055.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252206.1
locus_tag : CSB94_RS00010
name : WP_003092055.1
parent : gene-CSB94_RS00010
product : class-II fumarase/aspartase family protein
protein_id : WP_003092055.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271866/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP027166.1 Protein Homology CDS 1127 2578 . - 0 ID=cds-WP_003092055.1;Parent=gene-CSB94_RS00010;Dbxref=GenBank:WP_003092055.1;Name=WP_003092055.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252206.1;locus_tag=CSB94_RS00010;product=class-II fumarase/aspartase family protein;protein_id=WP_003092055.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB94_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB94_RS00015' for NZ_CP027166.1 Protein Homology CDS 2577 4010 -
dbxref : GenBank:WP_014603964.1
gbkey : CDS
gene : purB
go_function : N6-(1%2C2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity|0004018||IEA
go_process : purine ribonucleotide biosynthetic process|0009152||IEA
id : cds-WP_014603964.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252207.1
locus_tag : CSB94_RS00015
name : WP_014603964.1
ontology_term : GO:0009152,GO:0004018
parent : gene-CSB94_RS00015
product : adenylosuccinate lyase
protein_id : WP_014603964.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271866/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_CP027166.1 Protein Homology CDS |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271867/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271867/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271867/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271867/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271867/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM474_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM474_RS00010' for NZ_CP027538.1 Protein Homology CDS 299 1012 -
dbxref : GenBank:WP_003139068.1
gbkey : CDS
go_function : acyltransferase activity%2C transferring groups other than amino-acyl groups|0016747||IEA
id : cds-WP_003139068.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251234.1
locus_tag : AM474_RS00010
name : WP_003139068.1
ontology_term : GO:0016747
parent : gene-AM474_RS00010
product : GNAT family N-acetyltransferase
protein_id : WP_003139068.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271867/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP027538.1 Protein Homology CDS 300 1013 . - 0 ID=cds-WP_003139068.1;Parent=gene-AM474_RS00010;Dbxref=GenBank:WP_003139068.1;Name=WP_003139068.1;Ontology_term=GO:0016747;gbkey=CDS;go_function=acyltransferase activity%2C transferring groups other than amino-acyl groups|0016747||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251234.1;locus_tag=AM474_RS00010;product=GNAT family N-acetyltransferase;protein_id=WP_003139068.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM474_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM474_RS00015' for NZ_CP027538.1 Protein Homology CDS 1157 1969 +
dbxref : GenBank:WP_003089983.1
gbkey : CDS
gene : xthA
go_function : DNA binding|0003677||IEA,endonuclease activity|0004519||IEA,double-stranded DNA 3'-5' DNA exonuclease activity|0008311||IEA
go_process : DNA repair|0006281||IEA
id : cds-WP_003089983.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251235.1
locus_tag : AM474_RS00015
name : WP_003089983.1
ontology_term : GO:0006281,GO:0003677,GO:0004519,GO:0008311
parent : gene-AM474_RS00015
product : exodeoxyribonuclease III
protein_id : WP_003089983.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271867/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP027538.1 Protein Homology CDS 1158 1970 . + 0 ID=cds-WP_003089983.1;Parent=gene-AM474_RS00015;Dbxref=GenBank:WP_003089983.1;Name=WP_003089983.1;Ontology_term=GO:0006281,GO:0003677,GO:0004519,GO:0008311;gbkey=CDS;gene=xthA;go_function=DNA binding|0003677||IEA,endonuclease activity|0004519||IEA,double-stranded DNA 3'-5' DNA exonuclease activity|0008311||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251235.1;locus_tag=AM474_RS00015;product=exodeoxyribonuclease III;protein_id=WP_003089983.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM474_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM474_RS00020' for NZ_CP027538.1 Protein Homology CDS 2079 2510 -
dbxref : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271868/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271868/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271868/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271868/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271868/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ65_RS19570' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ65_RS19570' for NZ_RHSL01000010.1 Protein Homology CDS 0 4428 +
dbxref : GenBank:WP_185758318.1
gbkey : CDS
id : cds-WP_185758318.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_014833844.1
locus_tag : EGJ65_RS19570
name : WP_185758318.1
parent : gene-EGJ65_RS19570
partial : true
product : DUF637 domain-containing protein
protein_id : WP_185758318.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271868/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSL01000010.1 Protein Homology CDS 1 4429 . + 1 ID=cds-WP_185758318.1;Parent=gene-EGJ65_RS19570;Dbxref=GenBank:WP_185758318.1;Name=WP_185758318.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014833844.1;locus_tag=EGJ65_RS19570;partial=true;product=DUF637 domain-containing protein;protein_id=WP_185758318.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ65_RS19575' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ65_RS19575' for NZ_RHSL01000010.1 Protein Homology CDS 4439 4681 +
dbxref : GenBank:WP_003118488.1
gbkey : CDS
id : cds-WP_003118488.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003118488.1
locus_tag : EGJ65_RS19575
name : WP_003118488.1
parent : gene-EGJ65_RS19575
product : CPCC family cysteine-rich protein
protein_id : WP_003118488.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271868/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSL01000010.1 Protein Homology CDS 4440 4682 . + 0 ID=cds-WP_003118488.1;Parent=gene-EGJ65_RS19575;Dbxref=GenBank:WP_003118488.1;Name=WP_003118488.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003118488.1;locus_tag=EGJ65_RS19575;product=CPCC family cysteine-rich protein;protein_id=WP_003118488.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ65_RS19585' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ65_RS19585' for NZ_RHSL01000010.1 Protein Homology CDS 5037 5711 +
dbxref : GenBank:WP_260467039.1
gbkey : CDS
id : cds-WP_260467039.1
inference : COORDINATES: similar to AA sequence:RefSeq:YP_008719729.1
locus_tag : EGJ65_RS19585
name : WP_260467039.1
parent : gene-EGJ65_RS19585
product : transposase
protein_id : WP_260467039.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271868/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSL01000010.1 Protein Homology CDS 5038 5712 . + 0 ID=cds-WP_260467039.1;Parent=gene-EGJ65_RS19585;Dbxref=GenBank:WP_260467039.1;Name=WP_260467039.1;gbkey=CDS;inference=COORDINATES: similar to AA sequ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271869/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271869/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271869/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271869/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271869/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ79_RS15940' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ79_RS15940' for NZ_RHSV01000010.1 Protein Homology CDS 0 791 +
dbxref : GenBank:WP_162943521.1
gbkey : CDS
go_function : glutamine synthetase activity|0004356||IEA,ATP binding|0005524||IEA
go_process : glutamine biosynthetic process|0006542||IEA
id : cds-WP_162943521.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250730.1
locus_tag : EGJ79_RS15940
name : WP_162943521.1
ontology_term : GO:0006542,GO:0004356,GO:0005524
parent : gene-EGJ79_RS15940
partial : true
product : glutamine synthetase family protein
protein_id : WP_162943521.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271869/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSV01000010.1 Protein Homology CDS 1 792 . + 0 ID=cds-WP_162943521.1;Parent=gene-EGJ79_RS15940;Dbxref=GenBank:WP_162943521.1;Name=WP_162943521.1;Ontology_term=GO:0006542,GO:0004356,GO:0005524;gbkey=CDS;go_function=glutamine synthetase activity|0004356||IEA,ATP binding|0005524||IEA;go_process=glutamine biosynthetic process|0006542||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250730.1;locus_tag=EGJ79_RS15940;partial=true;product=glutamine synthetase family protein;protein_id=WP_162943521.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ79_RS15945' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ79_RS15945' for NZ_RHSV01000010.1 Protein Homology CDS 948 2318 +
dbxref : GenBank:WP_003106497.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
id : cds-WP_003106497.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250731.1
locus_tag : EGJ79_RS15945
name : WP_003106497.1
ontology_term : GO:0022857,GO:0016020
parent : gene-EGJ79_RS15945
product : APC family permease
protein_id : WP_003106497.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271869/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSV01000010.1 Protein Homology CDS 949 2319 . + 0 ID=cds-WP_003106497.1;Parent=gene-EGJ79_RS15945;Dbxref=GenBank:WP_003106497.1;Name=WP_003106497.1;Ontology_term=GO:0022857,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=transmembrane transporter activity|0022857||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250731.1;locus_tag=EGJ79_RS15945;product=APC family permease;protein_id=WP_003106497.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ79_RS15955' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ79_RS15955' for NZ_RHSV01000010.1 Protein Homology CDS 2806 4035 +
dbxref : GenBank:WP_003106499.1
gbkey : CDS
g |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271870/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271870/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271870/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271870/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271870/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC44_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC44_RS00005' for NZ_CP030327.1 Protein Homology CDS 97 1293 -
dbxref : GenBank:WP_003121674.1
gbkey : CDS
go_component : plasma membrane|0005886||IEA,membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003121674.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250782.1
locus_tag : CSC44_RS00005
name : WP_003121674.1
ontology_term : GO:0055085,GO:0022857,GO:0005886,GO:0016020
parent : gene-CSC44_RS00005
product : MFS transporter
protein_id : WP_003121674.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271870/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP030327.1 Protein Homology CDS 98 1294 . - 0 ID=cds-WP_003121674.1;Parent=gene-CSC44_RS00005;Dbxref=GenBank:WP_003121674.1;Name=WP_003121674.1;Ontology_term=GO:0055085,GO:0022857,GO:0005886,GO:0016020;gbkey=CDS;go_component=plasma membrane|0005886||IEA,membrane|0016020||IEA;go_function=transmembrane transporter activity|0022857||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250782.1;locus_tag=CSC44_RS00005;product=MFS transporter;protein_id=WP_003121674.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC44_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC44_RS00010' for NZ_CP030327.1 Protein Homology CDS 1280 2560 -
dbxref : GenBank:WP_112292486.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_112292486.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250781.1
locus_tag : CSC44_RS00010
name : WP_112292486.1
ontology_term : GO:0055085,GO:0022857,GO:0016020
parent : gene-CSC44_RS00010
product : MFS transporter
protein_id : WP_112292486.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271870/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP030327.1 Protein Homology CDS 1281 2561 . - 0 ID=cds-WP_112292486.1;Parent=gene-CSC44_RS00010;Dbxref=GenBank:WP_112292486.1;Name=WP_112292486.1;Ontology_term=GO:0055085,GO:0022857,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=transmembrane transporter activity|0022857||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250781.1;locus_tag=CSC44_RS00010;product=MFS transporter;protein_id=WP_112292486.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC44_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC44_RS00015' for NZ_CP030327. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271871/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271871/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271871/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271871/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271871/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_QHCK01000001.1:1-444) does not include 'gene-CSC34_RS00010' (NZ_QHCK01000001.1:499-1500). Created new gene 'null.2' (NZ_QHCK01000001.1:499-1500). File '/jetstream2/scratch/main/jobs/72271871/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 13 'NZ_QHCK01000001.1 RefSeq pseudogene 499 1500 . - . ID=gene-CSC34_RS00010;Name=CSC34_RS00010;gbkey=Gene;gene_biotype=pseudogene;locus_tag=CSC34_RS00010;pseudo=true'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC34_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC34_RS00015' for NZ_QHCK01000001.1 GeneMarkS-2+ CDS 1653 2045 -
dbxref : GenBank:WP_003088646.1
gbkey : CDS
id : cds-WP_003088646.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : CSC34_RS00015
name : WP_003088646.1
parent : gene-CSC34_RS00015
product : hypothetical protein
protein_id : WP_003088646.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271871/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_QHCK01000001.1 GeneMarkS-2+ CDS 1654 2046 . - 0 ID=cds-WP_003088646.1;Parent=gene-CSC34_RS00015;Dbxref=GenBank:WP_003088646.1;Name=WP_003088646.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=CSC34_RS00015;product=hypothetical protein;protein_id=WP_003088646.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC34_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC34_RS00020' for NZ_QHCK01000001.1 Protein Homology CDS 2178 2651 +
dbxref : GenBank:WP_003088649.1
gbkey : CDS
go_function : sequence-specific DNA binding|0043565||IEA
id : cds-WP_003088649.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250718.1
locus_tag : CSC34_RS00020
name : WP_003088649.1
ontology_term : GO:0043565
parent : gene-CSC34_RS00020
product : Lrp/AsnC family transcriptional regulator
protein_id : WP_003088649.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271871/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_QHCK01000001.1 Protein Homology CDS 2179 2652 . + 0 ID=cds-WP_003088649.1;Parent=gene-CSC34_RS00020;Dbxref=GenBank:WP_003088649.1;Name=WP_003088649.1;Ontology_term=GO:0043565;gbkey=CDS;go_function=sequence-specific DNA binding|0043565||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250718.1;locus_tag=CSC34_RS00020;product=Lrp/AsnC family transcriptional regulator;protein_id=WP_003088649.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC34_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC34_RS00025' for NZ_QHCK01000001.1 Protein Homology CDS 2675 2992 +
dbxref : GenBank:WP_003450460.1
gbkey : CDS
go_function : DNA binding|0003677||IEA
id : cds-WP_003450460.1
inference : COORDINATES: si |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271872/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271872/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271872/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271872/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271872/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC28_RS01415' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC28_RS01415' for NZ_CP029093.1 Protein Homology CDS 1573 2676 +
dbxref : GenBank:WP_034080765.1
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_034080765.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064722.1
locus_tag : CSC28_RS01415
name : WP_034080765.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-CSC28_RS01415
product : DNA polymerase III subunit beta
protein_id : WP_034080765.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271872/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029093.1 Protein Homology CDS 1574 2677 . + 0 ID=cds-WP_034080765.1;Parent=gene-CSC28_RS01415;Dbxref=GenBank:WP_034080765.1;Name=WP_034080765.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_064722.1;locus_tag=CSC28_RS01415;product=DNA polymerase III subunit beta;protein_id=WP_034080765.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC28_RS01425' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC28_RS01425' for NZ_CP029093.1 Protein Homology CDS 3792 6212 +
dbxref : GenBank:WP_011979039.1
gbkey : CDS
gene : gyrB
go_component : chromosome|0005694||IEA
go_function : DNA binding|0003677||IEA,DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA,ATP binding|0005524||IEA
go_process : DNA topological change|0006265||IEA
id : cds-WP_011979039.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064724.1
locus_tag : CSC28_RS01425
name : WP_011979039.1
ontology_term : GO:0006265,GO:0003677,GO:0003918,GO:0005524,GO:0005694
parent : gene-CSC28_RS01425
product : DNA topoisomerase (ATP-hydrolyzing) subunit B
protein_id : WP_011979039.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271872/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_CP029093.1 Protein Homology CDS 3793 6213 . + 0 ID=cds-WP_011979039.1;Parent=gene-CSC28_RS01425;Dbxref=GenBank:WP_011979039.1;Name=WP_011979039.1;Ontology_term=GO:0006265,GO:0003677,GO:0003918,GO:0005524,GO:0005694;gbkey=CDS;gene=gyrB;go_component=chromosome|0005694||IEA;go_function=DNA binding|0003677||IEA,DNA topoisomerase type II (double strand cut%2C ATP-hydrolyzing) activity|0003918||IEA,ATP binding|0005524||IEA;g |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271873/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271873/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271873/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271873/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271873/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC29_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC29_RS00005' for NZ_CP029090.1 Protein Homology CDS 6 1493 +
dbxref : GenBank:WP_003159318.1
gbkey : CDS
go_function : aldehyde dehydrogenase [NAD(P)+] activity|0004030||IEA
id : cds-WP_003159318.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252762.1
locus_tag : CSC29_RS00005
name : WP_003159318.1
ontology_term : GO:0004030
parent : gene-CSC29_RS00005
product : aldehyde dehydrogenase family protein
protein_id : WP_003159318.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271873/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_CP029090.1 Protein Homology CDS 7 1494 . + 0 ID=cds-WP_003159318.1;Parent=gene-CSC29_RS00005;Dbxref=GenBank:WP_003159318.1;Name=WP_003159318.1;Ontology_term=GO:0004030;gbkey=CDS;go_function=aldehyde dehydrogenase [NAD(P)+] activity|0004030||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252762.1;locus_tag=CSC29_RS00005;product=aldehyde dehydrogenase family protein;protein_id=WP_003159318.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC29_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC29_RS00010' for NZ_CP029090.1 Protein Homology CDS 1683 3173 +
dbxref : GenBank:WP_017001906.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : amino acid transmembrane transporter activity|0015171||IEA,transmembrane transporter activity|0022857||IEA
go_process : amino acid transport|0006865||IEA,transmembrane transport|0055085||IEA
id : cds-WP_017001906.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252761.1
locus_tag : CSC29_RS00010
name : WP_017001906.1
ontology_term : GO:0006865,GO:0055085,GO:0015171,GO:0022857,GO:0016020
parent : gene-CSC29_RS00010
product : APC family permease
protein_id : WP_017001906.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271873/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_CP029090.1 Protein Homology CDS 1684 3174 . + 0 ID=cds-WP_017001906.1;Parent=gene-CSC29_RS00010;Dbxref=GenBank:WP_017001906.1;Name=WP_017001906.1;Ontology_term=GO:0006865,GO:0055085,GO:0015171,GO:0022857,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=amino acid transmembrane transporter activity|0015171||IEA,transmembrane transporter activity|0022857||IEA;go_process=amino acid transport|0006865||IEA,transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252761.1;locus_tag=CSC29_RS00010;product=APC family permease;protein_id=WP_017001906.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSC29_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSC29_RS00015' for NZ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271874/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271874/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271874/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271874/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271874/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB95_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB95_RS00005' for NZ_PSQR01000001.1 Protein Homology CDS 0 2012 -
dbxref : GenBank:WP_106120712.1
gbkey : CDS
go_function : ATP binding|0005524||IEA
id : cds-WP_106120712.1
inference : COORDINATES: protein motif:HMM:NF015118.6
locus_tag : CSB95_RS00005
name : WP_106120712.1
ontology_term : GO:0005524
parent : gene-CSB95_RS00005
partial : true
product : VirB4 family type IV secretion/conjugal transfer ATPase
protein_id : WP_106120712.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271874/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_PSQR01000001.1 Protein Homology CDS 1 2013 . - 0 ID=cds-WP_106120712.1;Parent=gene-CSB95_RS00005;Dbxref=GenBank:WP_106120712.1;Name=WP_106120712.1;Ontology_term=GO:0005524;gbkey=CDS;go_function=ATP binding|0005524||IEA;inference=COORDINATES: protein motif:HMM:NF015118.6;locus_tag=CSB95_RS00005;partial=true;product=VirB4 family type IV secretion/conjugal transfer ATPase;protein_id=WP_106120712.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB95_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB95_RS00010' for NZ_PSQR01000001.1 Protein Homology CDS 2031 2327 -
dbxref : GenBank:WP_032180636.1
gbkey : CDS
id : cds-WP_032180636.1
inference : COORDINATES: protein motif:HMM:NF016820.6
locus_tag : CSB95_RS00010
name : WP_032180636.1
parent : gene-CSB95_RS00010
product : TrbC/VirB2 family protein
protein_id : WP_032180636.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271874/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_PSQR01000001.1 Protein Homology CDS 2032 2328 . - 0 ID=cds-WP_032180636.1;Parent=gene-CSB95_RS00010;Dbxref=GenBank:WP_032180636.1;Name=WP_032180636.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF016820.6;locus_tag=CSB95_RS00010;product=TrbC/VirB2 family protein;protein_id=WP_032180636.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-CSB95_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-CSB95_RS00015' for NZ_PSQR01000001.1 Protein Homology CDS 2305 2952 -
dbxref : GenBank:WP_000953528.1
gbkey : CDS
go_component : type IV secretion system complex|0043684||IEA
id : cds-WP_000953528.1
inference : COORDINATES: protein motif:HMM:NF013618.6
locus_tag : CSB95_RS00015
name : WP_000953528.1
ontology_term : GO:0043684
parent : gene-CSB95_RS00015
product : lytic transglycosylase domain-containing protein
protein_id : WP_000953528.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271874/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271875/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271875/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271875/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271875/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271875/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY961_RS30035' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY961_RS30035' for NZ_RXUG01000001.1 Protein Homology CDS 0 905 +
dbxref : GenBank:WP_148104771.1
gbkey : CDS
go_function : carbohydrate binding|0030246||IEA
id : cds-WP_148104771.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_014602871.1
locus_tag : DY961_RS30035
name : WP_148104771.1
ontology_term : GO:0030246
parent : gene-DY961_RS30035
partial : true
product : RHS repeat domain-containing protein
protein_id : WP_148104771.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271875/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUG01000001.1 Protein Homology CDS 1 906 . + 0 ID=cds-WP_148104771.1;Parent=gene-DY961_RS30035;Dbxref=GenBank:WP_148104771.1;Name=WP_148104771.1;Ontology_term=GO:0030246;gbkey=CDS;go_function=carbohydrate binding|0030246||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_014602871.1;locus_tag=DY961_RS30035;partial=true;product=RHS repeat domain-containing protein;protein_id=WP_148104771.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY961_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY961_RS00010' for NZ_RXUG01000001.1 GeneMarkS-2+ CDS 914 1153 +
dbxref : GenBank:WP_023101810.1
gbkey : CDS
id : cds-WP_023101810.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY961_RS00010
name : WP_023101810.1
parent : gene-DY961_RS00010
product : hypothetical protein
protein_id : WP_023101810.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271875/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUG01000001.1 GeneMarkS-2+ CDS 915 1154 . + 0 ID=cds-WP_023101810.1;Parent=gene-DY961_RS00010;Dbxref=GenBank:WP_023101810.1;Name=WP_023101810.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY961_RS00010;product=hypothetical protein;protein_id=WP_023101810.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY961_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY961_RS00025' for NZ_RXUG01000001.1 Protein Homology CDS 2146 3399 +
dbxref : GenBank:WP_003122406.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : O antigen polymerase activity|0008755||IEA
id : cds-WP_003122406.1
inference : COORDINATES: protein motif:HMM:TIGR04370.1
locus_tag : DY961_RS00025
name : WP_003122406.1
ontology_term : GO:0008755,GO:0016020
parent : gene-DY961_RS00025
product : O-antigen polymerase
protein_id : WP_003122406.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271875/working/snpeff_output/Pseudomonasaeruginosa/gen |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271876/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271876/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271876/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271876/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271876/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY986_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY986_RS00005' for NZ_RXVH01000001.1 Protein Homology CDS 389 2320 +
dbxref : GenBank:WP_010793418.1
gbkey : CDS
gene : eatR
id : cds-WP_010793418.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252710.1
locus_tag : DY986_RS00005
name : WP_010793418.1
parent : gene-DY986_RS00005
product : sigma-54-dependent transcriptional regulator EatR
protein_id : WP_010793418.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271876/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXVH01000001.1 Protein Homology CDS 390 2321 . + 0 ID=cds-WP_010793418.1;Parent=gene-DY986_RS00005;Dbxref=GenBank:WP_010793418.1;Name=WP_010793418.1;gbkey=CDS;gene=eatR;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252710.1;locus_tag=DY986_RS00005;product=sigma-54-dependent transcriptional regulator EatR;protein_id=WP_010793418.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY986_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY986_RS00010' for NZ_RXVH01000001.1 Protein Homology CDS 2478 3833 +
dbxref : GenBank:WP_003124067.1
gbkey : CDS
gene : mpl
go_function : acid-amino acid ligase activity|0016881||IEA
go_process : peptidoglycan biosynthetic process|0009252||IEA,cell wall organization|0071555||IEA
id : cds-WP_003124067.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252709.1
locus_tag : DY986_RS00010
name : WP_003124067.1
ontology_term : GO:0009252,GO:0071555,GO:0016881
parent : gene-DY986_RS00010
product : UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase
protein_id : WP_003124067.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271876/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXVH01000001.1 Protein Homology CDS 2479 3834 . + 0 ID=cds-WP_003124067.1;Parent=gene-DY986_RS00010;Dbxref=GenBank:WP_003124067.1;Name=WP_003124067.1;Ontology_term=GO:0009252,GO:0071555,GO:0016881;gbkey=CDS;gene=mpl;go_function=acid-amino acid ligase activity|0016881||IEA;go_process=peptidoglycan biosynthetic process|0009252||IEA,cell wall organization|0071555||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252709.1;locus_tag=DY986_RS00010;product=UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase;protein_id=WP_003124067.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY986_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY986_RS00015' for NZ_RXVH01000001.1 Protein Homology CDS 3842 4471 +
dbxref : GenBank:WP_003093227.1
gbkey : CDS
gene : ubiX
id : cds-WP_003093227.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252708.1
locu |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271877/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271877/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271877/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271877/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271877/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY937_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY937_RS00005' for NZ_RXTI01000001.1 Protein Homology CDS 0 512 -
dbxref : GenBank:WP_124137704.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA
id : cds-WP_124137704.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252711.1
locus_tag : DY937_RS00005
name : WP_124137704.1
ontology_term : GO:0016491
parent : gene-DY937_RS00005
partial : true
product : aldehyde dehydrogenase family protein
protein_id : WP_124137704.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271877/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTI01000001.1 Protein Homology CDS 1 513 . - 0 ID=cds-WP_124137704.1;Parent=gene-DY937_RS00005;Dbxref=GenBank:WP_124137704.1;Name=WP_124137704.1;Ontology_term=GO:0016491;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252711.1;locus_tag=DY937_RS00005;partial=true;product=aldehyde dehydrogenase family protein;protein_id=WP_124137704.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY937_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY937_RS00010' for NZ_RXTI01000001.1 Protein Homology CDS 851 2782 +
dbxref : GenBank:WP_023123718.1
gbkey : CDS
gene : eatR
id : cds-WP_023123718.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252710.1
locus_tag : DY937_RS00010
name : WP_023123718.1
parent : gene-DY937_RS00010
product : sigma-54-dependent transcriptional regulator EatR
protein_id : WP_023123718.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271877/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTI01000001.1 Protein Homology CDS 852 2783 . + 0 ID=cds-WP_023123718.1;Parent=gene-DY937_RS00010;Dbxref=GenBank:WP_023123718.1;Name=WP_023123718.1;gbkey=CDS;gene=eatR;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252710.1;locus_tag=DY937_RS00010;product=sigma-54-dependent transcriptional regulator EatR;protein_id=WP_023123718.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY937_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY937_RS00015' for NZ_RXTI01000001.1 Protein Homology CDS 2940 4295 +
dbxref : GenBank:WP_003093229.1
gbkey : CDS
gene : mpl
go_function : acid-amino acid ligase activity|0016881||IEA
go_process : peptidoglycan biosynthetic process|0009252||IEA,cell wall organization|0071555||IEA
id : cds-WP_003093229.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252709.1
locus_tag : DY937_RS00015
name : WP_003093229.1
ontology_term : GO:0009252,GO:0071555,GO:0016881
parent : gene-DY937_RS00015
|
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271878/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271878/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271878/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271878/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271878/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY963_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY963_RS00005' for NZ_RXUI01000001.1 Protein Homology CDS 0 1112 +
dbxref : GenBank:WP_148105188.1
gbkey : CDS
go_function : carbohydrate binding|0030246||IEA
id : cds-WP_148105188.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003146766.1
locus_tag : DY963_RS00005
name : WP_148105188.1
ontology_term : GO:0030246
parent : gene-DY963_RS00005
partial : true
product : RHS repeat domain-containing protein
protein_id : WP_148105188.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271878/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUI01000001.1 Protein Homology CDS 1 1113 . + 0 ID=cds-WP_148105188.1;Parent=gene-DY963_RS00005;Dbxref=GenBank:WP_148105188.1;Name=WP_148105188.1;Ontology_term=GO:0030246;gbkey=CDS;go_function=carbohydrate binding|0030246||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003146766.1;locus_tag=DY963_RS00005;partial=true;product=RHS repeat domain-containing protein;protein_id=WP_148105188.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY963_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY963_RS00010' for NZ_RXUI01000001.1 GeneMarkS-2+ CDS 1116 1631 +
dbxref : GenBank:WP_057380423.1
gbkey : CDS
id : cds-WP_057380423.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : DY963_RS00010
name : WP_057380423.1
parent : gene-DY963_RS00010
product : hypothetical protein
protein_id : WP_057380423.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271878/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUI01000001.1 GeneMarkS-2+ CDS 1117 1632 . + 0 ID=cds-WP_057380423.1;Parent=gene-DY963_RS00010;Dbxref=GenBank:WP_057380423.1;Name=WP_057380423.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=DY963_RS00010;product=hypothetical protein;protein_id=WP_057380423.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY963_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY963_RS00015' for NZ_RXUI01000001.1 Protein Homology CDS 2320 3573 +
dbxref : GenBank:WP_034075755.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : O antigen polymerase activity|0008755||IEA
id : cds-WP_034075755.1
inference : COORDINATES: protein motif:HMM:TIGR04370.1
locus_tag : DY963_RS00015
name : WP_034075755.1
ontology_term : GO:0008755,GO:0016020
parent : gene-DY963_RS00015
product : O-antigen polymerase
protein_id : WP_034075755.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271878/working/snpeff_output/Pseudomonasaeruginosa |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271879/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271879/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271879/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271879/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271879/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY949_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY949_RS00005' for NZ_RXTU01000001.1 Protein Homology CDS 282 3377 -
dbxref : GenBank:WP_073654786.1
gbkey : CDS
gene : dnaE2
id : cds-WP_073654786.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY949_RS00005
name : WP_073654786.1
parent : gene-DY949_RS00005
product : error-prone DNA polymerase
protein_id : WP_073654786.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271879/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTU01000001.1 Protein Homology CDS 283 3378 . - 0 ID=cds-WP_073654786.1;Parent=gene-DY949_RS00005;Dbxref=GenBank:WP_073654786.1;Name=WP_073654786.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY949_RS00005;product=error-prone DNA polymerase;protein_id=WP_073654786.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY949_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY949_RS00010' for NZ_RXTU01000001.1 Protein Homology CDS 3353 4768 -
dbxref : GenBank:WP_033993076.1
gbkey : CDS
id : cds-WP_033993076.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY949_RS00010
name : WP_033993076.1
parent : gene-DY949_RS00010
product : Y-family DNA polymerase
protein_id : WP_033993076.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271879/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTU01000001.1 Protein Homology CDS 3354 4769 . - 0 ID=cds-WP_033993076.1;Parent=gene-DY949_RS00010;Dbxref=GenBank:WP_033993076.1;Name=WP_033993076.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY949_RS00010;product=Y-family DNA polymerase;protein_id=WP_033993076.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY949_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY949_RS00015' for NZ_RXTU01000001.1 Protein Homology CDS 4776 5381 -
dbxref : GenBank:WP_031627677.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031627677.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003296675.1
locus_tag : DY949_RS00015
name : WP_031627677.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY949_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031627677.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271879/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTU01000001.1 Protein Homology CDS 4777 5382 . - 0 ID=cds-WP_031627677.1;Parent=gene-DY949_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271880/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271880/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271880/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271880/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271880/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY944_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY944_RS00005' for NZ_RXTP01000001.1 Protein Homology CDS 378 1349 +
dbxref : GenBank:WP_003096673.1
gbkey : CDS
gene : pstS
id : cds-WP_003096673.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254056.1
locus_tag : DY944_RS00005
name : WP_003096673.1
parent : gene-DY944_RS00005
product : phosphate ABC transporter substrate-binding protein PstS
protein_id : WP_003096673.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271880/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTP01000001.1 Protein Homology CDS 379 1350 . + 0 ID=cds-WP_003096673.1;Parent=gene-DY944_RS00005;Dbxref=GenBank:WP_003096673.1;Name=WP_003096673.1;gbkey=CDS;gene=pstS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254056.1;locus_tag=DY944_RS00005;product=phosphate ABC transporter substrate-binding protein PstS;protein_id=WP_003096673.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY944_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY944_RS00010' for NZ_RXTP01000001.1 Protein Homology CDS 1772 3805 +
dbxref : GenBank:WP_003123734.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003123734.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254055.1
locus_tag : DY944_RS00010
name : WP_003123734.1
ontology_term : GO:0055085,GO:0016020
parent : gene-DY944_RS00010
product : ABC transporter permease subunit
protein_id : WP_003123734.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271880/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTP01000001.1 Protein Homology CDS 1773 3806 . + 0 ID=cds-WP_003123734.1;Parent=gene-DY944_RS00010;Dbxref=GenBank:WP_003123734.1;Name=WP_003123734.1;Ontology_term=GO:0055085,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254055.1;locus_tag=DY944_RS00010;product=ABC transporter permease subunit;protein_id=WP_003123734.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY944_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY944_RS00015' for NZ_RXTP01000001.1 Protein Homology CDS 3825 5501 +
dbxref : GenBank:WP_003096667.1
gbkey : CDS
gene : pstA
go_component : plasma membrane|0005886||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ATPase-coupled phosphate ion transmembrane transporter activity|0015415||IEA
go_process : phosphate ion transport|0006817||IEA
id : cds-WP_003096667.1
inference : COORDINATES: |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271881/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271881/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271881/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271881/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271881/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ95_RS15800' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ95_RS15800' for NZ_RHSX01000010.1 Protein Homology CDS 316 1566 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGJ95_RS15800
name : WP_003096779.1
parent : gene-EGJ95_RS15800
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271881/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSX01000010.1 Protein Homology CDS 317 1567 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGJ95_RS15800;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGJ95_RS15800;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ95_RS15805' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ95_RS15805' for NZ_RHSX01000010.1 Protein Homology CDS 1660 1980 +
dbxref : GenBank:WP_023084796.1
gbkey : CDS
id : cds-WP_023084796.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGJ95_RS15805
name : WP_023084796.1
parent : gene-EGJ95_RS15805
product : sarcosine oxidase subunit delta
protein_id : WP_023084796.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271881/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSX01000010.1 Protein Homology CDS 1661 1981 . + 0 ID=cds-WP_023084796.1;Parent=gene-EGJ95_RS15805;Dbxref=GenBank:WP_023084796.1;Name=WP_023084796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGJ95_RS15805;product=sarcosine oxidase subunit delta;protein_id=WP_023084796.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ95_RS15810' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ95_RS15810' for NZ_RHSX01000010.1 Protein Homology CDS 1977 4994 +
dbxref : GenBank:WP_003162069.1
gbkey : CDS
id : cds-WP_003162069.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGJ95_RS15810
name : WP_003162069.1
parent : gene-EGJ95_RS15810
product : sarcosine oxidase subunit alpha
protein_id : WP_003162069.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271881/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSX01000010.1 Protein Homology CDS 1978 4995 . + 0 ID=cds-WP_003162069.1;Parent=gene-EGJ95_RS15810;Dbxref=GenBank:WP_003162069.1;Name=WP_003162069.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGJ95_RS15810;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271882/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271882/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271882/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:02 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271882/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:02 Reading file '/jetstream2/scratch/main/jobs/72271882/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ97_RS27755' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ97_RS27755' for NZ_RHSW01000100.1 Protein Homology CDS 0 593 -
dbxref : GenBank:WP_148103801.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA,NAD+ binding|0070403||IEA
id : cds-WP_148103801.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250035.1
locus_tag : EGJ97_RS27755
name : WP_148103801.1
ontology_term : GO:0016491,GO:0070403
parent : gene-EGJ97_RS27755
partial : true
product : SDR family NAD(P)-dependent oxidoreductase
protein_id : WP_148103801.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271882/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RHSW01000100.1 Protein Homology CDS 1 594 . - 0 ID=cds-WP_148103801.1;Parent=gene-EGJ97_RS27755;Dbxref=GenBank:WP_148103801.1;Name=WP_148103801.1;Ontology_term=GO:0016491,GO:0070403;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA,NAD+ binding|0070403||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250035.1;locus_tag=EGJ97_RS27755;partial=true;product=SDR family NAD(P)-dependent oxidoreductase;protein_id=WP_148103801.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ97_RS27760' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ97_RS27760' for NZ_RHSW01000100.1 Protein Homology CDS 689 1147 -
dbxref : GenBank:WP_003082771.1
gbkey : CDS
gene : pagP
id : cds-WP_003082771.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250034.1
locus_tag : EGJ97_RS27760
name : WP_003082771.1
parent : gene-EGJ97_RS27760
product : palmitoyltransferase PagP
protein_id : WP_003082771.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271882/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSW01000100.1 Protein Homology CDS 690 1148 . - 0 ID=cds-WP_003082771.1;Parent=gene-EGJ97_RS27760;Dbxref=GenBank:WP_003082771.1;Name=WP_003082771.1;gbkey=CDS;gene=pagP;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250034.1;locus_tag=EGJ97_RS27760;product=palmitoyltransferase PagP;protein_id=WP_003082771.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ97_RS27765' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ97_RS27765' for NZ_RHSW01000100.1 Protein Homology CDS 1599 2507 +
dbxref : GenBank:WP_003082770.1
gbkey : CDS
go_function : RNA binding|0003723||IEA,pseudouridine synthase activity|0009982||IEA
go_process : pseudouridine synthesis|0001522||IEA,RNA modification|0009451||IEA
id : cds-WP_003082770.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250033.1
locus_tag : EGJ97_RS27765
name : WP_003082770.1
ontology_term : GO:0001522,GO:0009451,GO:0003723,GO:00 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271883/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271883/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271883/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271883/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271883/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ90_RS15650' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ90_RS15650' for NZ_RHSU01000010.1 Protein Homology CDS 628 1878 +
dbxref : GenBank:WP_003096779.1
gbkey : CDS
id : cds-WP_003096779.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254103.1
locus_tag : EGJ90_RS15650
name : WP_003096779.1
parent : gene-EGJ90_RS15650
product : sarcosine oxidase subunit beta
protein_id : WP_003096779.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271883/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSU01000010.1 Protein Homology CDS 629 1879 . + 0 ID=cds-WP_003096779.1;Parent=gene-EGJ90_RS15650;Dbxref=GenBank:WP_003096779.1;Name=WP_003096779.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254103.1;locus_tag=EGJ90_RS15650;product=sarcosine oxidase subunit beta;protein_id=WP_003096779.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ90_RS15655' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ90_RS15655' for NZ_RHSU01000010.1 Protein Homology CDS 1972 2292 +
dbxref : GenBank:WP_023084796.1
gbkey : CDS
id : cds-WP_023084796.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254104.1
locus_tag : EGJ90_RS15655
name : WP_023084796.1
parent : gene-EGJ90_RS15655
product : sarcosine oxidase subunit delta
protein_id : WP_023084796.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271883/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSU01000010.1 Protein Homology CDS 1973 2293 . + 0 ID=cds-WP_023084796.1;Parent=gene-EGJ90_RS15655;Dbxref=GenBank:WP_023084796.1;Name=WP_023084796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254104.1;locus_tag=EGJ90_RS15655;product=sarcosine oxidase subunit delta;protein_id=WP_023084796.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ90_RS15660' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ90_RS15660' for NZ_RHSU01000010.1 Protein Homology CDS 2289 5306 +
dbxref : GenBank:WP_003162069.1
gbkey : CDS
id : cds-WP_003162069.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254105.1
locus_tag : EGJ90_RS15660
name : WP_003162069.1
parent : gene-EGJ90_RS15660
product : sarcosine oxidase subunit alpha
protein_id : WP_003162069.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271883/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_RHSU01000010.1 Protein Homology CDS 2290 5307 . + 0 ID=cds-WP_003162069.1;Parent=gene-EGJ90_RS15660;Dbxref=GenBank:WP_003162069.1;Name=WP_003162069.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254105.1;locus_tag=EGJ90_RS15660;product=sarcos |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271884/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271884/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271884/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271884/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271884/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ62_RS14050' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ62_RS14050' for NZ_RHSC01000010.1 Protein Homology CDS 768 2324 +
dbxref : GenBank:WP_017148916.1
gbkey : CDS
gene : tssA
id : cds-WP_017148916.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250347.1
locus_tag : EGJ62_RS14050
name : WP_017148916.1
parent : gene-EGJ62_RS14050
product : type VI secretion system protein TssA
protein_id : WP_017148916.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271884/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RHSC01000010.1 Protein Homology CDS 769 2325 . + 0 ID=cds-WP_017148916.1;Parent=gene-EGJ62_RS14050;Dbxref=GenBank:WP_017148916.1;Name=WP_017148916.1;gbkey=CDS;gene=tssA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250347.1;locus_tag=EGJ62_RS14050;product=type VI secretion system protein TssA;protein_id=WP_017148916.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ62_RS14055' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ62_RS14055' for NZ_RHSC01000010.1 Protein Homology CDS 2360 2866 +
dbxref : GenBank:WP_016851765.1
gbkey : CDS
gene : tssB
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_016851765.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250348.1
locus_tag : EGJ62_RS14055
name : WP_016851765.1
ontology_term : GO:0033103
parent : gene-EGJ62_RS14055
product : type VI secretion system contractile sheath small subunit
protein_id : WP_016851765.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271884/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RHSC01000010.1 Protein Homology CDS 2361 2867 . + 0 ID=cds-WP_016851765.1;Parent=gene-EGJ62_RS14055;Dbxref=GenBank:WP_016851765.1;Name=WP_016851765.1;Ontology_term=GO:0033103;gbkey=CDS;gene=tssB;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250348.1;locus_tag=EGJ62_RS14055;product=type VI secretion system contractile sheath small subunit;protein_id=WP_016851765.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-EGJ62_RS14060' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-EGJ62_RS14060' for NZ_RHSC01000010.1 Protein Homology CDS 2895 4370 +
dbxref : GenBank:WP_003087596.1
gbkey : CDS
gene : tssC
go_component : type VI protein secretion system complex|0033104||IEA
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_003087596.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250349.1
locus_tag : EGJ62_RS14060
name : WP_003087596.1
ontology_term : GO:0033103,GO: |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271885/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271885/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271885/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271885/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271885/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM433_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM433_RS00005' for NZ_MPBV01000001.1 Protein Homology CDS 482 2026 +
dbxref : GenBank:WP_003109151.1
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003109151.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064721.1
locus_tag : AM433_RS00005
name : WP_003109151.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-AM433_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003109151.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271885/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_MPBV01000001.1 Protein Homology CDS 483 2027 . + 0 ID=cds-WP_003109151.1;Parent=gene-AM433_RS00005;Dbxref=GenBank:WP_003109151.1;Name=WP_003109151.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_064721.1;locus_tag=AM433_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003109151.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM433_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM433_RS00010' for NZ_MPBV01000001.1 Protein Homology CDS 2055 3158 +
dbxref : GenBank:WP_003097262.1
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_003097262.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064722.1
locus_tag : AM433_RS00010
name : WP_003097262.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-AM433_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_003097262.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271885/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_MPBV01000001.1 Protein Homology CDS 2056 3159 . + 0 ID=cds-WP_003097262.1;Parent=gene-AM433_RS00010;Dbxref=GenBank:WP_003097262.1;Name=WP_003097262.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||I |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271886/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271886/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271886/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271886/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271886/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM487_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM487_RS00005' for NZ_MPBN01000001.1 Protein Homology CDS 0 1131 -
dbxref : GenBank:WP_071579570.1
gbkey : CDS
gene : pcnB
go_function : RNA binding|0003723||IEA,poly(A) RNA polymerase activity|1990817||IEA
go_process : polyadenylation-dependent RNA catabolic process|0043633||IEA
id : cds-WP_071579570.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253415.1
locus_tag : AM487_RS00005
name : WP_071579570.1
ontology_term : GO:0043633,GO:0003723,GO:1990817
parent : gene-AM487_RS00005
partial : true
product : polynucleotide adenylyltransferase PcnB
protein_id : WP_071579570.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271886/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_MPBN01000001.1 Protein Homology CDS 1 1132 . - 0 ID=cds-WP_071579570.1;Parent=gene-AM487_RS00005;Dbxref=GenBank:WP_071579570.1;Name=WP_071579570.1;Ontology_term=GO:0043633,GO:0003723,GO:1990817;gbkey=CDS;gene=pcnB;go_function=RNA binding|0003723||IEA,poly(A) RNA polymerase activity|1990817||IEA;go_process=polyadenylation-dependent RNA catabolic process|0043633||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253415.1;locus_tag=AM487_RS00005;partial=true;product=polynucleotide adenylyltransferase PcnB;protein_id=WP_071579570.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM487_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM487_RS00010' for NZ_MPBN01000001.1 Protein Homology CDS 2032 3468 -
dbxref : GenBank:WP_003123502.1
gbkey : CDS
gene : cbrB
id : cds-WP_003123502.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253414.1
locus_tag : AM487_RS00010
name : WP_003123502.1
parent : gene-AM487_RS00010
product : two-component system response regulator CbrB
protein_id : WP_003123502.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271886/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_MPBN01000001.1 Protein Homology CDS 2033 3469 . - 0 ID=cds-WP_003123502.1;Parent=gene-AM487_RS00010;Dbxref=GenBank:WP_003123502.1;Name=WP_003123502.1;gbkey=CDS;gene=cbrB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253414.1;locus_tag=AM487_RS00010;product=two-component system response regulator CbrB;protein_id=WP_003123502.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM487_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM487_RS00015' for NZ_MPBN01000001.1 Protein Homology CDS 3495 6446 -
dbxref : GenBank:WP_003095132.1
gbkey : CDS
gene : cbrA
id : cds-WP_003095132.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253413.1
locus_tag |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271887/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271887/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271887/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271887/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271887/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM473_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM473_RS00005' for NZ_MPBR01000001.1 Protein Homology CDS 482 2026 +
dbxref : GenBank:WP_003109151.1
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003109151.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064721.1
locus_tag : AM473_RS00005
name : WP_003109151.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-AM473_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003109151.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271887/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_MPBR01000001.1 Protein Homology CDS 483 2027 . + 0 ID=cds-WP_003109151.1;Parent=gene-AM473_RS00005;Dbxref=GenBank:WP_003109151.1;Name=WP_003109151.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_064721.1;locus_tag=AM473_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003109151.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM473_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM473_RS00010' for NZ_MPBR01000001.1 Protein Homology CDS 2055 3158 +
dbxref : GenBank:WP_016852300.1
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_016852300.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064722.1
locus_tag : AM473_RS00010
name : WP_016852300.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-AM473_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_016852300.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271887/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_MPBR01000001.1 Protein Homology CDS 2056 3159 . + 0 ID=cds-WP_016852300.1;Parent=gene-AM473_RS00010;Dbxref=GenBank:WP_016852300.1;Name=WP_016852300.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||I |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271888/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271888/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271888/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271888/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271888/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM484_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM484_RS00005' for NZ_MPBO01000001.1 Protein Homology CDS 482 2026 +
dbxref : GenBank:WP_003109151.1
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003109151.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064721.1
locus_tag : AM484_RS00005
name : WP_003109151.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-AM484_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003109151.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271888/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_MPBO01000001.1 Protein Homology CDS 483 2027 . + 0 ID=cds-WP_003109151.1;Parent=gene-AM484_RS00005;Dbxref=GenBank:WP_003109151.1;Name=WP_003109151.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_064721.1;locus_tag=AM484_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003109151.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM484_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM484_RS00010' for NZ_MPBO01000001.1 Protein Homology CDS 2055 3158 +
dbxref : GenBank:WP_003097262.1
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_003097262.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_064722.1
locus_tag : AM484_RS00010
name : WP_003097262.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-AM484_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_003097262.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271888/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_MPBO01000001.1 Protein Homology CDS 2056 3159 . + 0 ID=cds-WP_003097262.1;Parent=gene-AM484_RS00010;Dbxref=GenBank:WP_003097262.1;Name=WP_003097262.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||I |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271889/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271889/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271889/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271889/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271889/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM479_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM479_RS00005' for NZ_MPBQ01000001.1 Protein Homology CDS 120 347 -
dbxref : GenBank:WP_003100909.1
gbkey : CDS
id : cds-WP_003100909.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003100909.1
locus_tag : AM479_RS00005
name : WP_003100909.1
parent : gene-AM479_RS00005
product : hypothetical protein
protein_id : WP_003100909.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271889/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_MPBQ01000001.1 Protein Homology CDS 121 348 . - 0 ID=cds-WP_003100909.1;Parent=gene-AM479_RS00005;Dbxref=GenBank:WP_003100909.1;Name=WP_003100909.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003100909.1;locus_tag=AM479_RS00005;product=hypothetical protein;protein_id=WP_003100909.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM479_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM479_RS00010' for NZ_MPBQ01000001.1 Protein Homology CDS 347 697 -
dbxref : GenBank:WP_042858037.1
gbkey : CDS
id : cds-WP_042858037.1
inference : COORDINATES: protein motif:HMM:NF036589.6
locus_tag : AM479_RS00010
name : WP_042858037.1
parent : gene-AM479_RS00010
product : DNA-binding protein
protein_id : WP_042858037.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271889/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_MPBQ01000001.1 Protein Homology CDS 348 698 . - 0 ID=cds-WP_042858037.1;Parent=gene-AM479_RS00010;Dbxref=GenBank:WP_042858037.1;Name=WP_042858037.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF036589.6;locus_tag=AM479_RS00010;product=DNA-binding protein;protein_id=WP_042858037.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM479_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM479_RS00015' for NZ_MPBQ01000001.1 GeneMarkS-2+ CDS 703 960 -
dbxref : GenBank:WP_071580081.1
gbkey : CDS
id : cds-WP_071580081.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : AM479_RS00015
name : WP_071580081.1
parent : gene-AM479_RS00015
product : hypothetical protein
protein_id : WP_071580081.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271889/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_MPBQ01000001.1 GeneMarkS-2+ CDS 704 961 . - 0 ID=cds-WP_071580081.1;Parent=gene-AM479_RS00015;Dbxref=GenBank:WP_071580081.1;Name=WP_071580081.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=AM479_RS00015;product=hypothetical protein;protein_id=WP_071580081.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM479_RS00025' is |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271890/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271890/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271890/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271890/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271890/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM471_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM471_RS00005' for NZ_MPBS01000001.1 Protein Homology CDS 0 284 +
dbxref : GenBank:WP_218163261.1
gbkey : CDS
go_function : disulfide oxidoreductase activity|0015036||IEA
id : cds-WP_218163261.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_011871455.1
locus_tag : AM471_RS00005
name : WP_218163261.1
ontology_term : GO:0015036
parent : gene-AM471_RS00005
partial : true
product : DsbA family protein
protein_id : WP_218163261.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271890/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_MPBS01000001.1 Protein Homology CDS 1 285 . + 0 ID=cds-WP_218163261.1;Parent=gene-AM471_RS00005;Dbxref=GenBank:WP_218163261.1;Name=WP_218163261.1;Ontology_term=GO:0015036;gbkey=CDS;go_function=disulfide oxidoreductase activity|0015036||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_011871455.1;locus_tag=AM471_RS00005;partial=true;product=DsbA family protein;protein_id=WP_218163261.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM471_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM471_RS00015' for NZ_MPBS01000001.1 Protein Homology CDS 1109 1555 +
dbxref : GenBank:WP_003158648.1
gbkey : CDS
id : cds-WP_003158648.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_006226031.1
locus_tag : AM471_RS00015
name : WP_003158648.1
parent : gene-AM471_RS00015
product : TIGR03757 family integrating conjugative element protein
protein_id : WP_003158648.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271890/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_MPBS01000001.1 Protein Homology CDS 1110 1556 . + 0 ID=cds-WP_003158648.1;Parent=gene-AM471_RS00015;Dbxref=GenBank:WP_003158648.1;Name=WP_003158648.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_006226031.1;locus_tag=AM471_RS00015;product=TIGR03757 family integrating conjugative element protein;protein_id=WP_003158648.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM471_RS34135' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM471_RS34135' for NZ_MPBS01000001.1 Protein Homology CDS 2509 3903 +
dbxref : GenBank:WP_003158650.1
gbkey : CDS
id : cds-WP_003158650.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_006226032.1
locus_tag : AM471_RS34135
name : WP_003158650.1
parent : gene-AM471_RS34135
product : integrating conjugative element protein
protein_id : WP_003158650.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271890/working/snpeff_output/Pseudomonasaerugin |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271891/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271891/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271891/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271891/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271891/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM482_RS34060' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM482_RS34060' for NZ_MPBP01000001.1 Protein Homology CDS 476 1249 +
dbxref : GenBank:WP_254796046.1
gbkey : CDS
id : cds-WP_254796046.1
inference : COORDINATES: protein motif:HMM:NF023295.6
locus_tag : AM482_RS34060
name : WP_254796046.1
parent : gene-AM482_RS34060
product : type I restriction enzyme subunit R domain-containing protein
protein_id : WP_254796046.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271891/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_MPBP01000001.1 Protein Homology CDS 477 1250 . + 0 ID=cds-WP_254796046.1;Parent=gene-AM482_RS34060;Dbxref=GenBank:WP_254796046.1;Name=WP_254796046.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF023295.6;locus_tag=AM482_RS34060;product=type I restriction enzyme subunit R domain-containing protein;protein_id=WP_254796046.1;transl_table=11'
WARNING_GENE_NOT_FOUND: Gene 'null' (NZ_MPBP01000001.1:1-480) does not include 'gene-AM482_RS34065' (NZ_MPBP01000001.1:1205-1815). Created new gene 'null.2' (NZ_MPBP01000001.1:1205-1815). File '/jetstream2/scratch/main/jobs/72271891/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 15 'NZ_MPBP01000001.1 RefSeq pseudogene 1205 1815 . + . ID=gene-AM482_RS34065;Name=AM482_RS34065;gbkey=Gene;gene_biotype=pseudogene;locus_tag=AM482_RS34065;old_locus_tag=AM482_000003;pseudo=true'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM482_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM482_RS00010' for NZ_MPBP01000001.1 GeneMarkS-2+ CDS 1820 2611 +
dbxref : GenBank:WP_042855636.1
gbkey : CDS
id : cds-WP_042855636.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : AM482_RS00010
name : WP_042855636.1
parent : gene-AM482_RS00010
product : hypothetical protein
protein_id : WP_042855636.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271891/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_MPBP01000001.1 GeneMarkS-2+ CDS 1821 2612 . + 0 ID=cds-WP_042855636.1;Parent=gene-AM482_RS00010;Dbxref=GenBank:WP_042855636.1;Name=WP_042855636.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=AM482_RS00010;product=hypothetical protein;protein_id=WP_042855636.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AM482_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AM482_RS00015' for NZ_MPBP01000001.1 Protein Homology CDS 2558 2863 -
dbxref : GenBank:WP_071567699.1
gbkey : CDS
go_function : nuclease activity|0004518||IEA
id : cds-WP_071567699.1
inference : COORDINATES: protein motif:HMM:NF013691.6
locus_tag : AM482_RS00015
name : WP_071567699.1
ontology_term : GO:0004518
parent : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271892/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271892/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271892/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271892/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271892/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS58_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS58_RS00005' for NZ_JTQZ01000001.1 Protein Homology CDS 0 99 -
dbxref : GenBank:WP_033970086.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,transposase activity|0004803||IEA
go_process : DNA transposition|0006313||IEA
id : cds-WP_033970086.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_076612095.1
locus_tag : NS58_RS00005
name : WP_033970086.1
ontology_term : GO:0006313,GO:0003677,GO:0004803
parent : gene-NS58_RS00005
partial : true
product : transposase
protein_id : WP_033970086.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271892/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQZ01000001.1 Protein Homology CDS 1 100 . - 0 ID=cds-WP_033970086.1;Parent=gene-NS58_RS00005;Dbxref=GenBank:WP_033970086.1;Name=WP_033970086.1;Ontology_term=GO:0006313,GO:0003677,GO:0004803;gbkey=CDS;go_function=DNA binding|0003677||IEA,transposase activity|0004803||IEA;go_process=DNA transposition|0006313||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_076612095.1;locus_tag=NS58_RS00005;partial=true;product=transposase;protein_id=WP_033970086.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS58_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS58_RS00010' for NZ_JTQZ01000001.1 GeneMarkS-2+ CDS 383 1738 -
dbxref : GenBank:WP_003161875.1
gbkey : CDS
id : cds-WP_003161875.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : NS58_RS00010
name : WP_003161875.1
parent : gene-NS58_RS00010
product : hypothetical protein
protein_id : WP_003161875.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271892/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQZ01000001.1 GeneMarkS-2+ CDS 384 1739 . - 0 ID=cds-WP_003161875.1;Parent=gene-NS58_RS00010;Dbxref=GenBank:WP_003161875.1;Name=WP_003161875.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=NS58_RS00010;product=hypothetical protein;protein_id=WP_003161875.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS58_RS31825' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS58_RS31825' for NZ_JTQZ01000001.1 Protein Homology CDS 2184 3647 -
dbxref : GenBank:WP_071557695.1
gbkey : CDS
id : cds-WP_071557695.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003119219.1
locus_tag : NS58_RS31825
name : WP_071557695.1
parent : gene-NS58_RS31825
product : YecA family protein
protein_id : WP_071557695.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271892/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271893/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271893/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271893/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271893/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271893/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-TN45_RS34285' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-TN45_RS34285' for NZ_JYGC02000015.1 Protein Homology CDS 0 874 +
dbxref : GenBank:WP_079452760.1
gbkey : CDS
id : cds-WP_079452760.1
inference : COORDINATES: protein motif:HMM:NF015831.6
locus_tag : TN45_RS34285
name : WP_079452760.1
parent : gene-TN45_RS34285
partial : true
product : YadA-like family protein
protein_id : WP_079452760.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271893/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JYGC02000015.1 Protein Homology CDS 1 875 . + 2 ID=cds-WP_079452760.1;Parent=gene-TN45_RS34285;Dbxref=GenBank:WP_079452760.1;Name=WP_079452760.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF015831.6;locus_tag=TN45_RS34285;partial=true;product=YadA-like family protein;protein_id=WP_079452760.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-TN45_RS30970' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-TN45_RS30970' for NZ_JYGC02000015.1 Protein Homology CDS 877 1209 +
dbxref : GenBank:WP_044727380.1
gbkey : CDS
id : cds-WP_044727380.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_000716758.1
locus_tag : TN45_RS30970
name : WP_044727380.1
parent : gene-TN45_RS30970
product : TrbM/KikA/MpfK family conjugal transfer protein
protein_id : WP_044727380.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271893/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JYGC02000015.1 Protein Homology CDS 878 1210 . + 0 ID=cds-WP_044727380.1;Parent=gene-TN45_RS30970;Dbxref=GenBank:WP_044727380.1;Name=WP_044727380.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_000716758.1;locus_tag=TN45_RS30970;product=TrbM/KikA/MpfK family conjugal transfer protein;protein_id=WP_044727380.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-TN45_RS30975' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-TN45_RS30975' for NZ_JYGC02000015.1 Protein Homology CDS 1321 3516 +
dbxref : GenBank:WP_044727381.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,DNA topoisomerase activity|0003916||IEA
go_process : DNA topological change|0006265||IEA
id : cds-WP_044727381.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003142893.1
locus_tag : TN45_RS30975
name : WP_044727381.1
ontology_term : GO:0006265,GO:0003677,GO:0003916
parent : gene-TN45_RS30975
product : type IA DNA topoisomerase
protein_id : WP_044727381.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271893/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JYGC02000015.1 Protein Homology CDS 132 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271894/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271894/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271894/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271894/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271894/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS51_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS51_RS00005' for NZ_JTRG01000001.1 Protein Homology CDS 441 3536 -
dbxref : GenBank:WP_073647890.1
gbkey : CDS
gene : dnaE2
id : cds-WP_073647890.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : NS51_RS00005
name : WP_073647890.1
parent : gene-NS51_RS00005
product : error-prone DNA polymerase
protein_id : WP_073647890.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271894/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 15 'NZ_JTRG01000001.1 Protein Homology CDS 442 3537 . - 0 ID=cds-WP_073647890.1;Parent=gene-NS51_RS00005;Dbxref=GenBank:WP_073647890.1;Name=WP_073647890.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=NS51_RS00005;product=error-prone DNA polymerase;protein_id=WP_073647890.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS51_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS51_RS00010' for NZ_JTRG01000001.1 Protein Homology CDS 3512 4927 -
dbxref : GenBank:WP_023087780.1
gbkey : CDS
go_function : damaged DNA binding|0003684||IEA,DNA-directed DNA polymerase activity|0003887||IEA,metal ion binding|0046872||IEA
go_process : DNA replication|0006260||IEA,DNA repair|0006281||IEA
id : cds-WP_023087780.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : NS51_RS00010
name : WP_023087780.1
ontology_term : GO:0006260,GO:0006281,GO:0003684,GO:0003887,GO:0046872
parent : gene-NS51_RS00010
product : Y-family DNA polymerase
protein_id : WP_023087780.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271894/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 17 'NZ_JTRG01000001.1 Protein Homology CDS 3513 4928 . - 0 ID=cds-WP_023087780.1;Parent=gene-NS51_RS00010;Dbxref=GenBank:WP_023087780.1;Name=WP_023087780.1;Ontology_term=GO:0006260,GO:0006281,GO:0003684,GO:0003887,GO:0046872;gbkey=CDS;go_function=damaged DNA binding|0003684||IEA,DNA-directed DNA polymerase activity|0003887||IEA,metal ion binding|0046872||IEA;go_process=DNA replication|0006260||IEA,DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=NS51_RS00010;product=Y-family DNA polymerase;protein_id=WP_023087780.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS51_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS51_RS00015' for NZ_JTRG01000001.1 Protein Homology CDS 4935 5540 -
dbxref : GenBank:WP_031627677.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031627677.1
inference : COORDINATES: similar to |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271895/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271895/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271895/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271895/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271895/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS63_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS63_RS00005' for NZ_JTQU01000001.1 Protein Homology CDS 0 214 +
dbxref : GenBank:WP_033971772.1
gbkey : CDS
go_process : DNA integration|0015074||IEA
id : cds-WP_033971772.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_086558210.1
locus_tag : NS63_RS00005
name : WP_033971772.1
ontology_term : GO:0015074
parent : gene-NS63_RS00005
partial : true
product : integrase core domain-containing protein
protein_id : WP_033971772.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271895/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQU01000001.1 Protein Homology CDS 1 215 . + 2 ID=cds-WP_033971772.1;Parent=gene-NS63_RS00005;Dbxref=GenBank:WP_033971772.1;Name=WP_033971772.1;Ontology_term=GO:0015074;gbkey=CDS;go_process=DNA integration|0015074||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_086558210.1;locus_tag=NS63_RS00005;partial=true;product=integrase core domain-containing protein;protein_id=WP_033971772.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS63_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS63_RS00010' for NZ_JTQU01000001.1 Protein Homology CDS 265 1065 -
dbxref : GenBank:WP_031761375.1
gbkey : CDS
id : cds-WP_031761375.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_016254335.1
locus_tag : NS63_RS00010
name : WP_031761375.1
parent : gene-NS63_RS00010
product : glycosyltransferase
protein_id : WP_031761375.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271895/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQU01000001.1 Protein Homology CDS 266 1066 . - 0 ID=cds-WP_031761375.1;Parent=gene-NS63_RS00010;Dbxref=GenBank:WP_031761375.1;Name=WP_031761375.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016254335.1;locus_tag=NS63_RS00010;product=glycosyltransferase;protein_id=WP_031761375.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS63_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS63_RS00015' for NZ_JTQU01000001.1 Protein Homology CDS 1062 2183 -
dbxref : GenBank:WP_031640407.1
gbkey : CDS
id : cds-WP_031640407.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003137189.1
locus_tag : NS63_RS00015
name : WP_031640407.1
parent : gene-NS63_RS00015
product : hypothetical protein
protein_id : WP_031640407.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271895/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQU01000001.1 Protein Homology CDS 1063 2184 . - 0 ID=cds-WP_031640407.1;Parent=gene-NS6 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271896/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271896/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271896/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271896/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271896/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS56_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS56_RS00005' for NZ_JTRB01000001.1 Protein Homology CDS 0 317 +
dbxref : GenBank:WP_033945769.1
gbkey : CDS
go_process : DNA integration|0015074||IEA
id : cds-WP_033945769.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_086558210.1
locus_tag : NS56_RS00005
name : WP_033945769.1
ontology_term : GO:0015074
parent : gene-NS56_RS00005
partial : true
product : integrase core domain-containing protein
protein_id : WP_033945769.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271896/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTRB01000001.1 Protein Homology CDS 1 318 . + 0 ID=cds-WP_033945769.1;Parent=gene-NS56_RS00005;Dbxref=GenBank:WP_033945769.1;Name=WP_033945769.1;Ontology_term=GO:0015074;gbkey=CDS;go_process=DNA integration|0015074||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_086558210.1;locus_tag=NS56_RS00005;partial=true;product=integrase core domain-containing protein;protein_id=WP_033945769.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS56_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS56_RS00020' for NZ_JTRB01000001.1 Protein Homology CDS 1218 1892 -
dbxref : GenBank:WP_003111415.1
gbkey : CDS
gene : queC
go_process : queuosine biosynthetic process|0008616||IEA
id : cds-WP_003111415.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249667.1
locus_tag : NS56_RS00020
name : WP_003111415.1
ontology_term : GO:0008616
parent : gene-NS56_RS00020
product : 7-cyano-7-deazaguanine synthase QueC
protein_id : WP_003111415.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271896/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 19 'NZ_JTRB01000001.1 Protein Homology CDS 1219 1893 . - 0 ID=cds-WP_003111415.1;Parent=gene-NS56_RS00020;Dbxref=GenBank:WP_003111415.1;Name=WP_003111415.1;Ontology_term=GO:0008616;gbkey=CDS;gene=queC;go_process=queuosine biosynthetic process|0008616||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249667.1;locus_tag=NS56_RS00020;product=7-cyano-7-deazaguanine synthase QueC;protein_id=WP_003111415.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS56_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS56_RS00025' for NZ_JTRB01000001.1 Protein Homology CDS 1908 2555 -
dbxref : GenBank:WP_003112571.1
gbkey : CDS
gene : queE
go_function : 4 iron%2C 4 sulfur cluster binding|0051539||IEA,S-adenosyl-L-methionine binding|1904047||IEA
go_process : tRNA modification|0006400||IEA
id : cds-WP_003112571.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003155997.1
locus_tag |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271897/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271897/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271897/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271897/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271897/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS50_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS50_RS00005' for NZ_JTRH01000001.1 Protein Homology CDS 0 444 +
dbxref : GenBank:WP_033875249.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_process : signal transduction|0007165||IEA
id : cds-WP_033875249.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253000.1
locus_tag : NS50_RS00005
name : WP_033875249.1
ontology_term : GO:0007165,GO:0016020
parent : gene-NS50_RS00005
partial : true
product : methyl-accepting chemotaxis protein
protein_id : WP_033875249.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271897/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTRH01000001.1 Protein Homology CDS 1 445 . + 1 ID=cds-WP_033875249.1;Parent=gene-NS50_RS00005;Dbxref=GenBank:WP_033875249.1;Name=WP_033875249.1;Ontology_term=GO:0007165,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_process=signal transduction|0007165||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253000.1;locus_tag=NS50_RS00005;partial=true;product=methyl-accepting chemotaxis protein;protein_id=WP_033875249.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS50_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS50_RS00010' for NZ_JTRH01000001.1 Protein Homology CDS 762 1877 +
dbxref : GenBank:WP_034034915.1
gbkey : CDS
go_function : glycosyltransferase activity|0016757||IEA
go_process : protein glycosylation|0006486||IEA
id : cds-WP_034034915.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253001.1
locus_tag : NS50_RS00010
name : WP_034034915.1
ontology_term : GO:0006486,GO:0016757
parent : gene-NS50_RS00010
product : glycosyltransferase family 4 protein
protein_id : WP_034034915.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271897/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTRH01000001.1 Protein Homology CDS 763 1878 . + 0 ID=cds-WP_034034915.1;Parent=gene-NS50_RS00010;Dbxref=GenBank:WP_034034915.1;Name=WP_034034915.1;Ontology_term=GO:0006486,GO:0016757;gbkey=CDS;go_function=glycosyltransferase activity|0016757||IEA;go_process=protein glycosylation|0006486||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253001.1;locus_tag=NS50_RS00010;product=glycosyltransferase family 4 protein;protein_id=WP_034034915.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS50_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS50_RS00015' for NZ_JTRH01000001.1 Protein Homology CDS 1870 2631 +
dbxref : GenBank:WP_003101179.1
gbkey : CDS
id : cds-WP_003101179.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253002.1
locus_tag : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271898/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271898/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271898/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271898/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271898/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS53_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS53_RS00005' for NZ_JTRE01000001.1 Protein Homology CDS 104 997 -
dbxref : GenBank:WP_003114492.1
gbkey : CDS
id : cds-WP_003114492.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252123.1
locus_tag : NS53_RS00005
name : WP_003114492.1
parent : gene-NS53_RS00005
product : LysR family transcriptional regulator
protein_id : WP_003114492.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271898/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTRE01000001.1 Protein Homology CDS 105 998 . - 0 ID=cds-WP_003114492.1;Parent=gene-NS53_RS00005;Dbxref=GenBank:WP_003114492.1;Name=WP_003114492.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252123.1;locus_tag=NS53_RS00005;product=LysR family transcriptional regulator;protein_id=WP_003114492.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS53_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS53_RS00010' for NZ_JTRE01000001.1 Protein Homology CDS 1093 1482 +
dbxref : GenBank:WP_003091885.1
gbkey : CDS
go_component : membrane|0016020||IEA
id : cds-WP_003091885.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252122.1
locus_tag : NS53_RS00010
name : WP_003091885.1
ontology_term : GO:0016020
parent : gene-NS53_RS00010
product : CidA/LrgA family protein
protein_id : WP_003091885.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271898/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTRE01000001.1 Protein Homology CDS 1094 1483 . + 0 ID=cds-WP_003091885.1;Parent=gene-NS53_RS00010;Dbxref=GenBank:WP_003091885.1;Name=WP_003091885.1;Ontology_term=GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252122.1;locus_tag=NS53_RS00010;product=CidA/LrgA family protein;protein_id=WP_003091885.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS53_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS53_RS00015' for NZ_JTRE01000001.1 Protein Homology CDS 1469 2155 +
dbxref : GenBank:WP_003102323.1
gbkey : CDS
go_component : plasma membrane|0005886||IEA
id : cds-WP_003102323.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252121.1
locus_tag : NS53_RS00015
name : WP_003102323.1
ontology_term : GO:0005886
parent : gene-NS53_RS00015
product : LrgB family protein
protein_id : WP_003102323.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271898/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTRE01000001.1 Protein Homology CDS 1470 2156 . + 0 ID=cds-WP_003102323.1;Parent=gene-NS53_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271899/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271899/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271899/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271899/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271899/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS54_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS54_RS00005' for NZ_JTRD01000001.1 Protein Homology CDS 0 378 +
dbxref : GenBank:WP_033985398.1
gbkey : CDS
go_function : iron-sulfur cluster binding|0051536||IEA
id : cds-WP_033985398.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253504.1
locus_tag : NS54_RS00005
name : WP_033985398.1
ontology_term : GO:0051536
parent : gene-NS54_RS00005
partial : true
product : YkgJ family cysteine cluster protein
protein_id : WP_033985398.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271899/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTRD01000001.1 Protein Homology CDS 1 379 . + 1 ID=cds-WP_033985398.1;Parent=gene-NS54_RS00005;Dbxref=GenBank:WP_033985398.1;Name=WP_033985398.1;Ontology_term=GO:0051536;gbkey=CDS;go_function=iron-sulfur cluster binding|0051536||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253504.1;locus_tag=NS54_RS00005;partial=true;product=YkgJ family cysteine cluster protein;protein_id=WP_033985398.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS54_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS54_RS00010' for NZ_JTRD01000001.1 Protein Homology CDS 381 1817 -
dbxref : GenBank:WP_004365413.1
gbkey : CDS
go_function : glycosyltransferase activity|0016757||IEA
id : cds-WP_004365413.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253505.1
locus_tag : NS54_RS00010
name : WP_004365413.1
ontology_term : GO:0016757
parent : gene-NS54_RS00010
product : ArnT family glycosyltransferase
protein_id : WP_004365413.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271899/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTRD01000001.1 Protein Homology CDS 382 1818 . - 0 ID=cds-WP_004365413.1;Parent=gene-NS54_RS00010;Dbxref=GenBank:WP_004365413.1;Name=WP_004365413.1;Ontology_term=GO:0016757;gbkey=CDS;go_function=glycosyltransferase activity|0016757||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253505.1;locus_tag=NS54_RS00010;product=ArnT family glycosyltransferase;protein_id=WP_004365413.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS54_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS54_RS00015' for NZ_JTRD01000001.1 Protein Homology CDS 1814 2788 -
dbxref : GenBank:WP_003107470.1
gbkey : CDS
go_function : glycosyltransferase activity|0016757||IEA
id : cds-WP_003107470.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253506.1
locus_tag : NS54_RS00015
name : WP_003107470.1
ontology_term : GO:0016757
parent : gene-NS54_RS00015
product : glycosyltransferase family 2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271900/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271900/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271900/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271900/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271900/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS52_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS52_RS00005' for NZ_JTRF01000001.1 Protein Homology CDS 0 1747 -
dbxref : GenBank:WP_034044754.1
gbkey : CDS
gene : pctA
id : cds-WP_034044754.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252999.1
locus_tag : NS52_RS00005
name : WP_034044754.1
parent : gene-NS52_RS00005
partial : true
product : methyl-accepting chemotaxis protein PctA
protein_id : WP_034044754.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271900/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTRF01000001.1 Protein Homology CDS 1 1748 . - 0 ID=cds-WP_034044754.1;Parent=gene-NS52_RS00005;Dbxref=GenBank:WP_034044754.1;Name=WP_034044754.1;gbkey=CDS;gene=pctA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252999.1;locus_tag=NS52_RS00005;partial=true;product=methyl-accepting chemotaxis protein PctA;protein_id=WP_034044754.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS52_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS52_RS00010' for NZ_JTRF01000001.1 Protein Homology CDS 2147 3637 +
dbxref : GenBank:WP_003114975.1
gbkey : CDS
go_function : ATP binding|0005524||IEA
id : cds-WP_003114975.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252998.1
locus_tag : NS52_RS00010
name : WP_003114975.1
ontology_term : GO:0005524
parent : gene-NS52_RS00010
product : helicase HerA-like C-terminal domain-containing protein
protein_id : WP_003114975.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271900/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTRF01000001.1 Protein Homology CDS 2148 3638 . + 0 ID=cds-WP_003114975.1;Parent=gene-NS52_RS00010;Dbxref=GenBank:WP_003114975.1;Name=WP_003114975.1;Ontology_term=GO:0005524;gbkey=CDS;go_function=ATP binding|0005524||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252998.1;locus_tag=NS52_RS00010;product=helicase HerA-like C-terminal domain-containing protein;protein_id=WP_003114975.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS52_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS52_RS00015' for NZ_JTRF01000001.1 Protein Homology CDS 3741 5639 -
dbxref : GenBank:WP_003163018.1
gbkey : CDS
gene : pctC
id : cds-WP_003163018.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252997.1
locus_tag : NS52_RS00015
name : WP_003163018.1
parent : gene-NS52_RS00015
product : methyl-accepting chemotaxis protein PctC
protein_id : WP_003163018.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271900/working/snpeff_output/Pseudomonasa |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271901/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271901/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271901/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271901/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271901/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT03_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT03_RS00005' for NZ_JTPG01000001.1 Protein Homology CDS 0 812 +
dbxref : GenBank:WP_034008589.1
gbkey : CDS
gene : tssI
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_034008589.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015503835.1
locus_tag : NT03_RS00005
name : WP_034008589.1
ontology_term : GO:0033103
parent : gene-NT03_RS00005
partial : true
product : type VI secretion system tip protein TssI/VgrG
protein_id : WP_034008589.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271901/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPG01000001.1 Protein Homology CDS 1 813 . + 0 ID=cds-WP_034008589.1;Parent=gene-NT03_RS00005;Dbxref=GenBank:WP_034008589.1;Name=WP_034008589.1;Ontology_term=GO:0033103;gbkey=CDS;gene=tssI;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015503835.1;locus_tag=NT03_RS00005;partial=true;product=type VI secretion system tip protein TssI/VgrG;protein_id=WP_034008589.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT03_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT03_RS00010' for NZ_JTPG01000001.1 Protein Homology CDS 802 1683 +
dbxref : GenBank:WP_031686219.1
gbkey : CDS
id : cds-WP_031686219.1
inference : COORDINATES: protein motif:HMM:NF024894.6
locus_tag : NT03_RS00010
name : WP_031686219.1
parent : gene-NT03_RS00010
product : DUF4123 domain-containing protein
protein_id : WP_031686219.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271901/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPG01000001.1 Protein Homology CDS 803 1684 . + 0 ID=cds-WP_031686219.1;Parent=gene-NT03_RS00010;Dbxref=GenBank:WP_031686219.1;Name=WP_031686219.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF024894.6;locus_tag=NT03_RS00010;product=DUF4123 domain-containing protein;protein_id=WP_031686219.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT03_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT03_RS00015' for NZ_JTPG01000001.1 Protein Homology CDS 1680 5204 +
dbxref : GenBank:WP_031686218.1
gbkey : CDS
id : cds-WP_031686218.1
inference : COORDINATES: protein motif:HMM:NF042700.4
locus_tag : NT03_RS00015
name : WP_031686218.1
parent : gene-NT03_RS00015
product : toxin VasX
protein_id : WP_031686218.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271901/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271902/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271902/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271902/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271902/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271902/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT02_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT02_RS00010' for NZ_JTPH01000001.1 Protein Homology CDS 899 1684 -
dbxref : GenBank:WP_003159513.1
gbkey : CDS
go_component : cytoplasm|0005737||IEA
go_function : isomerase activity|0016853||IEA
go_process : biosynthetic process|0009058||IEA
id : cds-WP_003159513.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_016562182.1
locus_tag : NT02_RS00010
name : WP_003159513.1
ontology_term : GO:0009058,GO:0016853,GO:0005737
parent : gene-NT02_RS00010
product : PhzF family phenazine biosynthesis protein
protein_id : WP_003159513.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271902/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPH01000001.1 Protein Homology CDS 900 1685 . - 0 ID=cds-WP_003159513.1;Parent=gene-NT02_RS00010;Dbxref=GenBank:WP_003159513.1;Name=WP_003159513.1;Ontology_term=GO:0009058,GO:0016853,GO:0005737;gbkey=CDS;go_component=cytoplasm|0005737||IEA;go_function=isomerase activity|0016853||IEA;go_process=biosynthetic process|0009058||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_016562182.1;locus_tag=NT02_RS00010;product=PhzF family phenazine biosynthesis protein;protein_id=WP_003159513.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT02_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT02_RS00015' for NZ_JTPH01000001.1 Protein Homology CDS 1880 3364 -
dbxref : GenBank:WP_003143284.1
gbkey : CDS
gene : glpK
go_function : glycerol kinase activity|0004370||IEA
go_process : glycerol-3-phosphate metabolic process|0006072||IEA
id : cds-WP_003143284.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252269.1
locus_tag : NT02_RS00015
name : WP_003143284.1
ontology_term : GO:0006072,GO:0004370
parent : gene-NT02_RS00015
product : glycerol kinase GlpK
protein_id : WP_003143284.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271902/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPH01000001.1 Protein Homology CDS 1881 3365 . - 0 ID=cds-WP_003143284.1;Parent=gene-NT02_RS00015;Dbxref=GenBank:WP_003143284.1;Name=WP_003143284.1;Ontology_term=GO:0006072,GO:0004370;gbkey=CDS;gene=glpK;go_function=glycerol kinase activity|0004370||IEA;go_process=glycerol-3-phosphate metabolic process|0006072||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252269.1;locus_tag=NT02_RS00015;product=glycerol kinase GlpK;protein_id=WP_003143284.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT02_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT02_RS00020' for NZ_JTPH01000001.1 Protein Homology CDS 3428 3898 -
dbxref : GenBank:WP_003092163.1
gbkey : CDS
gene : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271903/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271903/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271903/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271903/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271903/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT01_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT01_RS00010' for NZ_JTPI01000001.1 Protein Homology CDS 488 1420 -
dbxref : GenBank:WP_003082652.1
gbkey : CDS
id : cds-WP_003082652.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249987.1
locus_tag : NT01_RS00010
name : WP_003082652.1
parent : gene-NT01_RS00010
product : D-2-hydroxyacid dehydrogenase
protein_id : WP_003082652.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271903/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPI01000001.1 Protein Homology CDS 489 1421 . - 0 ID=cds-WP_003082652.1;Parent=gene-NT01_RS00010;Dbxref=GenBank:WP_003082652.1;Name=WP_003082652.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249987.1;locus_tag=NT01_RS00010;product=D-2-hydroxyacid dehydrogenase;protein_id=WP_003082652.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT01_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT01_RS00015' for NZ_JTPI01000001.1 Protein Homology CDS 1675 1968 -
dbxref : GenBank:WP_003082651.1
gbkey : CDS
id : cds-WP_003082651.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249986.1
locus_tag : NT01_RS00015
name : WP_003082651.1
parent : gene-NT01_RS00015
product : YcgL domain-containing protein
protein_id : WP_003082651.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271903/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTPI01000001.1 Protein Homology CDS 1676 1969 . - 0 ID=cds-WP_003082651.1;Parent=gene-NT01_RS00015;Dbxref=GenBank:WP_003082651.1;Name=WP_003082651.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249986.1;locus_tag=NT01_RS00015;product=YcgL domain-containing protein;protein_id=WP_003082651.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT01_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT01_RS00020' for NZ_JTPI01000001.1 Protein Homology CDS 1965 3089 -
dbxref : GenBank:WP_003145300.1
gbkey : CDS
gene : rnd
go_function : 3'-5' exonuclease activity|0008408||IEA,ribonuclease D activity|0033890||IEA
go_process : RNA processing|0006396||IEA
id : cds-WP_003145300.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249985.1
locus_tag : NT01_RS00020
name : WP_003145300.1
ontology_term : GO:0006396,GO:0008408,GO:0033890
parent : gene-NT01_RS00020
product : ribonuclease D
protein_id : WP_003145300.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271903/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_JTPI01000001.1 Protein Homology CDS 1966 3090 . - 0 ID=cds-WP_003145300.1;Parent=gene-NT01_RS00020;Dbxr |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271904/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271904/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271904/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271904/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271904/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT00_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT00_RS00005' for NZ_JTPJ01000001.1 Protein Homology CDS 116 709 -
dbxref : GenBank:WP_003084527.1
gbkey : CDS
gene : rdgB
go_function : dITP diphosphatase activity|0035870||IEA,XTP diphosphatase activity|0036222||IEA
go_process : DNA repair|0006281||IEA
id : cds-WP_003084527.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249078.1
locus_tag : NT00_RS00005
name : WP_003084527.1
ontology_term : GO:0006281,GO:0035870,GO:0036222
parent : gene-NT00_RS00005
product : RdgB/HAM1 family non-canonical purine NTP pyrophosphatase
protein_id : WP_003084527.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271904/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPJ01000001.1 Protein Homology CDS 117 710 . - 0 ID=cds-WP_003084527.1;Parent=gene-NT00_RS00005;Dbxref=GenBank:WP_003084527.1;Name=WP_003084527.1;Ontology_term=GO:0006281,GO:0035870,GO:0036222;gbkey=CDS;gene=rdgB;go_function=dITP diphosphatase activity|0035870||IEA,XTP diphosphatase activity|0036222||IEA;go_process=DNA repair|0006281||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249078.1;locus_tag=NT00_RS00005;product=RdgB/HAM1 family non-canonical purine NTP pyrophosphatase;protein_id=WP_003084527.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT00_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT00_RS00010' for NZ_JTPJ01000001.1 Protein Homology CDS 706 1125 -
dbxref : GenBank:WP_003084528.1
gbkey : CDS
id : cds-WP_003084528.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249079.1
locus_tag : NT00_RS00010
name : WP_003084528.1
parent : gene-NT00_RS00010
product : DUF4426 domain-containing protein
protein_id : WP_003084528.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271904/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPJ01000001.1 Protein Homology CDS 707 1126 . - 0 ID=cds-WP_003084528.1;Parent=gene-NT00_RS00010;Dbxref=GenBank:WP_003084528.1;Name=WP_003084528.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249079.1;locus_tag=NT00_RS00010;product=DUF4426 domain-containing protein;protein_id=WP_003084528.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NT00_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NT00_RS00015' for NZ_JTPJ01000001.1 Protein Homology CDS 1257 1877 -
dbxref : GenBank:WP_003084530.1
gbkey : CDS
gene : metW
go_process : methionine biosynthetic process|0009086||IEA
id : cds-WP_003084530.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249080.1
locus_tag : NT00_RS00015
name : WP_003084530.1
ontology_term : GO:0009086
parent : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271905/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271905/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271905/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271905/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271905/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS97_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS97_RS00005' for NZ_JTPM01000001.1 Protein Homology CDS 162 1454 +
dbxref : GenBank:WP_023088869.1
gbkey : CDS
id : cds-WP_023088869.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249418.1
locus_tag : NS97_RS00005
name : WP_023088869.1
parent : gene-NS97_RS00005
product : hypothetical protein
protein_id : WP_023088869.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271905/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPM01000001.1 Protein Homology CDS 163 1455 . + 0 ID=cds-WP_023088869.1;Parent=gene-NS97_RS00005;Dbxref=GenBank:WP_023088869.1;Name=WP_023088869.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249418.1;locus_tag=NS97_RS00005;product=hypothetical protein;protein_id=WP_023088869.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS97_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS97_RS00010' for NZ_JTPM01000001.1 Protein Homology CDS 1454 2437 +
dbxref : GenBank:WP_034024252.1
gbkey : CDS
id : cds-WP_034024252.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249419.1
locus_tag : NS97_RS00010
name : WP_034024252.1
parent : gene-NS97_RS00010
product : phage integrase
protein_id : WP_034024252.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271905/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPM01000001.1 Protein Homology CDS 1455 2438 . + 0 ID=cds-WP_034024252.1;Parent=gene-NS97_RS00010;Dbxref=GenBank:WP_034024252.1;Name=WP_034024252.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249419.1;locus_tag=NS97_RS00010;product=phage integrase;protein_id=WP_034024252.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS97_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS97_RS00015' for NZ_JTPM01000001.1 Protein Homology CDS 2651 2902 +
dbxref : GenBank:WP_003114155.1
gbkey : CDS
id : cds-WP_003114155.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003114155.1
locus_tag : NS97_RS00015
name : WP_003114155.1
parent : gene-NS97_RS00015
product : type II toxin-antitoxin system Phd/YefM family antitoxin
protein_id : WP_003114155.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271905/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTPM01000001.1 Protein Homology CDS 2652 2903 . + 0 ID=cds-WP_003114155.1;Parent=gene-NS97_RS00015;Dbxref=GenBank:WP_003114155.1;Name=WP_003114155.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003114155.1;locus_tag=NS97_RS00015;product=type II toxin-antitoxin system Phd/YefM famil |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271906/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271906/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271906/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271906/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271906/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS96_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS96_RS00005' for NZ_JTPN01000001.1 Protein Homology CDS 0 1905 +
dbxref : GenBank:WP_033945796.1
gbkey : CDS
id : cds-WP_033945796.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248953.1
locus_tag : NS96_RS00005
name : WP_033945796.1
parent : gene-NS96_RS00005
partial : true
product : DUF2345 domain-containing protein
protein_id : WP_033945796.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271906/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPN01000001.1 Protein Homology CDS 1 1906 . + 1 ID=cds-WP_033945796.1;Parent=gene-NS96_RS00005;Dbxref=GenBank:WP_033945796.1;Name=WP_033945796.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248953.1;locus_tag=NS96_RS00005;partial=true;product=DUF2345 domain-containing protein;protein_id=WP_033945796.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS96_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS96_RS00010' for NZ_JTPN01000001.1 Protein Homology CDS 1909 2406 +
dbxref : GenBank:WP_003118123.1
gbkey : CDS
id : cds-WP_003118123.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248952.1
locus_tag : NS96_RS00010
name : WP_003118123.1
parent : gene-NS96_RS00010
product : hypothetical protein
protein_id : WP_003118123.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271906/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPN01000001.1 Protein Homology CDS 1910 2407 . + 0 ID=cds-WP_003118123.1;Parent=gene-NS96_RS00010;Dbxref=GenBank:WP_003118123.1;Name=WP_003118123.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248952.1;locus_tag=NS96_RS00010;product=hypothetical protein;protein_id=WP_003118123.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS96_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS96_RS00015' for NZ_JTPN01000001.1 Protein Homology CDS 2403 4559 +
dbxref : GenBank:WP_003118122.1
gbkey : CDS
id : cds-WP_003118122.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248951.1
locus_tag : NS96_RS00015
name : WP_003118122.1
parent : gene-NS96_RS00015
product : T6SS effector phospholipase Tle3 domain-containing protein
protein_id : WP_003118122.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271906/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTPN01000001.1 Protein Homology CDS 2404 4560 . + 0 ID=cds-WP_003118122.1;Parent=gene-NS96_RS00015;Dbxref=GenBank:WP_003118122.1;Name=WP_003118122.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:Ref |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271907/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271907/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271907/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271907/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271907/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS92_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS92_RS00015' for NZ_JTPR01000001.1 Protein Homology CDS 2038 2757 +
dbxref : GenBank:WP_003114657.1
gbkey : CDS
gene : tagT
id : cds-WP_003114657.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248763.1
locus_tag : NS92_RS00015
name : WP_003114657.1
parent : gene-NS92_RS00015
product : type IV secretion associated ABC transporter ATP-binding protein TagT
protein_id : WP_003114657.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271907/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTPR01000001.1 Protein Homology CDS 2039 2758 . + 0 ID=cds-WP_003114657.1;Parent=gene-NS92_RS00015;Dbxref=GenBank:WP_003114657.1;Name=WP_003114657.1;gbkey=CDS;gene=tagT;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248763.1;locus_tag=NS92_RS00015;product=type IV secretion associated ABC transporter ATP-binding protein TagT;protein_id=WP_003114657.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS92_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS92_RS00020' for NZ_JTPR01000001.1 Protein Homology CDS 2757 3956 +
dbxref : GenBank:WP_003083634.1
gbkey : CDS
gene : tagS
id : cds-WP_003083634.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248762.1
locus_tag : NS92_RS00020
name : WP_003083634.1
parent : gene-NS92_RS00020
product : type IV secretion associated ABC transporter permease TagS
protein_id : WP_003083634.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271907/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 18 'NZ_JTPR01000001.1 Protein Homology CDS 2758 3957 . + 0 ID=cds-WP_003083634.1;Parent=gene-NS92_RS00020;Dbxref=GenBank:WP_003083634.1;Name=WP_003083634.1;gbkey=CDS;gene=tagS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248762.1;locus_tag=NS92_RS00020;product=type IV secretion associated ABC transporter permease TagS;protein_id=WP_003083634.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS92_RS00025' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS92_RS00025' for NZ_JTPR01000001.1 Protein Homology CDS 3949 5661 +
dbxref : GenBank:WP_034070190.1
gbkey : CDS
gene : tagR
id : cds-WP_034070190.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248761.1
locus_tag : NS92_RS00025
name : WP_034070190.1
parent : gene-NS92_RS00025
product : type VI secretion system-associated regulator TagR
protein_id : WP_034070190.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271907/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 20 'NZ_JTPR01000001.1 Protein Homology CDS 3950 5662 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271908/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271908/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271908/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271908/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271908/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS90_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS90_RS00005' for NZ_JTPT01000001.1 Protein Homology CDS 24 1985 +
dbxref : GenBank:WP_052154562.1
gbkey : CDS
gene : betT
go_component : membrane|0016020||IEA
go_function : transmembrane transporter activity|0022857||IEA
go_process : nitrogen compound transport|0071705||IEA
id : cds-WP_052154562.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252622.1
locus_tag : NS90_RS00005
name : WP_052154562.1
ontology_term : GO:0071705,GO:0022857,GO:0016020
parent : gene-NS90_RS00005
product : choline BCCT transporter BetT
protein_id : WP_052154562.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271908/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPT01000001.1 Protein Homology CDS 25 1986 . + 0 ID=cds-WP_052154562.1;Parent=gene-NS90_RS00005;Dbxref=GenBank:WP_052154562.1;Name=WP_052154562.1;Ontology_term=GO:0071705,GO:0022857,GO:0016020;gbkey=CDS;gene=betT;go_component=membrane|0016020||IEA;go_function=transmembrane transporter activity|0022857||IEA;go_process=nitrogen compound transport|0071705||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252622.1;locus_tag=NS90_RS00005;product=choline BCCT transporter BetT;protein_id=WP_052154562.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS90_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS90_RS00010' for NZ_JTPT01000001.1 Protein Homology CDS 2093 4129 -
dbxref : GenBank:WP_003114310.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : oligopeptide transmembrane transporter activity|0035673||IEA
go_process : oligopeptide transport|0006857||IEA
id : cds-WP_003114310.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252623.1
locus_tag : NS90_RS00010
name : WP_003114310.1
ontology_term : GO:0006857,GO:0035673,GO:0016020
parent : gene-NS90_RS00010
product : OPT family oligopeptide transporter
protein_id : WP_003114310.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271908/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPT01000001.1 Protein Homology CDS 2094 4130 . - 0 ID=cds-WP_003114310.1;Parent=gene-NS90_RS00010;Dbxref=GenBank:WP_003114310.1;Name=WP_003114310.1;Ontology_term=GO:0006857,GO:0035673,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=oligopeptide transmembrane transporter activity|0035673||IEA;go_process=oligopeptide transport|0006857||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252623.1;locus_tag=NS90_RS00010;product=OPT family oligopeptide transporter;protein_id=WP_003114310.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS90_RS00015' is a Gene instead of a transcript. Created tran |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271909/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271909/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271909/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271909/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271909/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS89_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS89_RS00005' for NZ_JTPU01000001.1 Protein Homology CDS 0 580 -
dbxref : GenBank:WP_043495842.1
gbkey : CDS
go_function : carboxylic ester hydrolase activity|0052689||IEA
id : cds-WP_043495842.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251931.1
locus_tag : NS89_RS00005
name : WP_043495842.1
ontology_term : GO:0052689
parent : gene-NS89_RS00005
partial : true
product : patatin-like phospholipase family protein
protein_id : WP_043495842.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271909/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPU01000001.1 Protein Homology CDS 1 581 . - 0 ID=cds-WP_043495842.1;Parent=gene-NS89_RS00005;Dbxref=GenBank:WP_043495842.1;Name=WP_043495842.1;Ontology_term=GO:0052689;gbkey=CDS;go_function=carboxylic ester hydrolase activity|0052689||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251931.1;locus_tag=NS89_RS00005;partial=true;product=patatin-like phospholipase family protein;protein_id=WP_043495842.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS89_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS89_RS00010' for NZ_JTPU01000001.1 Protein Homology CDS 648 1586 -
dbxref : GenBank:WP_016852629.1
gbkey : CDS
id : cds-WP_016852629.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251932.1
locus_tag : NS89_RS00010
name : WP_016852629.1
parent : gene-NS89_RS00010
product : lipid A biosynthesis lauroyl acyltransferase
protein_id : WP_016852629.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271909/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPU01000001.1 Protein Homology CDS 649 1587 . - 0 ID=cds-WP_016852629.1;Parent=gene-NS89_RS00010;Dbxref=GenBank:WP_016852629.1;Name=WP_016852629.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251932.1;locus_tag=NS89_RS00010;product=lipid A biosynthesis lauroyl acyltransferase;protein_id=WP_016852629.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS89_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS89_RS00015' for NZ_JTPU01000001.1 Protein Homology CDS 1746 2537 +
dbxref : GenBank:WP_016852628.1
gbkey : CDS
gene : minC
go_function : enzyme inhibitor activity|0004857||IEA
go_process : division septum site selection|0000918||IEA,regulation of cell septum assembly|1901891||IEA
id : cds-WP_016852628.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251933.1
locus_tag : NS89_RS00015
name : WP_016852628.1
ontology_term : GO:0000918,GO:1901891,GO:0004857
parent : gene-NS89_RS00015
product |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271910/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271910/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271910/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271910/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271910/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS57_RS33810' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS57_RS33810' for NZ_JTRA01000001.1 Protein Homology CDS 0 110 -
dbxref : GenBank:WP_153570549.1
gbkey : CDS
go_component : cytochrome complex|0070069||IEA
go_function : electron transfer activity|0009055||IEA
go_process : aerobic electron transport chain|0019646||IEA
id : cds-WP_153570549.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252619.1
locus_tag : NS57_RS33810
name : WP_153570549.1
ontology_term : GO:0019646,GO:0009055,GO:0070069
parent : gene-NS57_RS33810
partial : true
product : cytochrome ubiquinol oxidase subunit I
protein_id : WP_153570549.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271910/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTRA01000001.1 Protein Homology CDS 1 111 . - 0 ID=cds-WP_153570549.1;Parent=gene-NS57_RS33810;Dbxref=GenBank:WP_153570549.1;Name=WP_153570549.1;Ontology_term=GO:0019646,GO:0009055,GO:0070069;gbkey=CDS;go_component=cytochrome complex|0070069||IEA;go_function=electron transfer activity|0009055||IEA;go_process=aerobic electron transport chain|0019646||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252619.1;locus_tag=NS57_RS33810;partial=true;product=cytochrome ubiquinol oxidase subunit I;protein_id=WP_153570549.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS57_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS57_RS00005' for NZ_JTRA01000001.1 Protein Homology CDS 346 1482 -
dbxref : GenBank:WP_033996472.1
gbkey : CDS
go_function : glutamate-cysteine ligase activity|0004357||IEA
go_process : cellular modified amino acid biosynthetic process|0042398||IEA
id : cds-WP_033996472.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012075878.1
locus_tag : NS57_RS00005
name : WP_033996472.1
ontology_term : GO:0042398,GO:0004357
parent : gene-NS57_RS00005
product : carboxylate-amine ligase
protein_id : WP_033996472.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271910/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTRA01000001.1 Protein Homology CDS 347 1483 . - 0 ID=cds-WP_033996472.1;Parent=gene-NS57_RS00005;Dbxref=GenBank:WP_033996472.1;Name=WP_033996472.1;Ontology_term=GO:0042398,GO:0004357;gbkey=CDS;go_function=glutamate-cysteine ligase activity|0004357||IEA;go_process=cellular modified amino acid biosynthetic process|0042398||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_012075878.1;locus_tag=NS57_RS00005;product=carboxylate-amine ligase;protein_id=WP_033996472.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS57_RS00010' is a Gene instead of a transcript. Created transcript |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271911/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271911/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271911/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271911/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271911/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS59_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS59_RS00010' for NZ_JTQY01000001.1 Protein Homology CDS 353 1729 +
dbxref : GenBank:WP_003112071.1
gbkey : CDS
go_function : L-serine ammonia-lyase activity|0003941||IEA
go_process : gluconeogenesis|0006094||IEA
id : cds-WP_003112071.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251133.1
locus_tag : NS59_RS00010
name : WP_003112071.1
ontology_term : GO:0006094,GO:0003941
parent : gene-NS59_RS00010
product : L-serine ammonia-lyase
protein_id : WP_003112071.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271911/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQY01000001.1 Protein Homology CDS 354 1730 . + 0 ID=cds-WP_003112071.1;Parent=gene-NS59_RS00010;Dbxref=GenBank:WP_003112071.1;Name=WP_003112071.1;Ontology_term=GO:0006094,GO:0003941;gbkey=CDS;go_function=L-serine ammonia-lyase activity|0003941||IEA;go_process=gluconeogenesis|0006094||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251133.1;locus_tag=NS59_RS00010;product=L-serine ammonia-lyase;protein_id=WP_003112071.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS59_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS59_RS00015' for NZ_JTQY01000001.1 Protein Homology CDS 1823 2944 +
dbxref : GenBank:WP_003122380.1
gbkey : CDS
gene : gcvT
go_function : aminomethyltransferase activity|0004047||IEA
go_process : glycine catabolic process|0006546||IEA
id : cds-WP_003122380.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251132.1
locus_tag : NS59_RS00015
name : WP_003122380.1
ontology_term : GO:0006546,GO:0004047
parent : gene-NS59_RS00015
product : glycine cleavage system aminomethyltransferase GcvT
protein_id : WP_003122380.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271911/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQY01000001.1 Protein Homology CDS 1824 2945 . + 0 ID=cds-WP_003122380.1;Parent=gene-NS59_RS00015;Dbxref=GenBank:WP_003122380.1;Name=WP_003122380.1;Ontology_term=GO:0006546,GO:0004047;gbkey=CDS;gene=gcvT;go_function=aminomethyltransferase activity|0004047||IEA;go_process=glycine catabolic process|0006546||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251132.1;locus_tag=NS59_RS00015;product=glycine cleavage system aminomethyltransferase GcvT;protein_id=WP_003122380.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS59_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS59_RS00020' for NZ_JTQY01000001.1 Protein Homology CDS 2990 3865 -
dbxref : GenBank:WP_003119384.1
gbkey : CDS
id : cds-WP_003119384.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271912/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271912/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271912/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271912/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271912/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS61_RS33095' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS61_RS33095' for NZ_JTQW01000001.1 GeneMarkS-2+ CDS 25 174 -
dbxref : GenBank:WP_023082394.1
gbkey : CDS
id : cds-WP_023082394.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : NS61_RS33095
name : WP_023082394.1
parent : gene-NS61_RS33095
product : hypothetical protein
protein_id : WP_023082394.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271912/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQW01000001.1 GeneMarkS-2+ CDS 26 175 . - 0 ID=cds-WP_023082394.1;Parent=gene-NS61_RS33095;Dbxref=GenBank:WP_023082394.1;Name=WP_023082394.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=NS61_RS33095;product=hypothetical protein;protein_id=WP_023082394.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS61_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS61_RS00005' for NZ_JTQW01000001.1 Protein Homology CDS 339 1688 -
dbxref : GenBank:WP_016852718.1
gbkey : CDS
id : cds-WP_016852718.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251419.1
locus_tag : NS61_RS00005
name : WP_016852718.1
parent : gene-NS61_RS00005
product : hypothetical protein
protein_id : WP_016852718.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271912/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQW01000001.1 Protein Homology CDS 340 1689 . - 0 ID=cds-WP_016852718.1;Parent=gene-NS61_RS00005;Dbxref=GenBank:WP_016852718.1;Name=WP_016852718.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251419.1;locus_tag=NS61_RS00005;product=hypothetical protein;protein_id=WP_016852718.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS61_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS61_RS00010' for NZ_JTQW01000001.1 Protein Homology CDS 1685 7981 -
dbxref : GenBank:WP_023083426.1
gbkey : CDS
id : cds-WP_023083426.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003143792.1
locus_tag : NS61_RS00010
name : WP_023083426.1
parent : gene-NS61_RS00010
product : AAA domain-containing protein
protein_id : WP_023083426.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271912/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQW01000001.1 Protein Homology CDS 1686 7982 . - 0 ID=cds-WP_023083426.1;Parent=gene-NS61_RS00010;Dbxref=GenBank:WP_023083426.1;Name=WP_023083426.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003143792.1;locus_tag=NS61_RS00010;product=AAA domain-containing protein;protein_id=WP_023083426.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271913/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271913/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271913/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271913/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271913/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS60_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS60_RS00005' for NZ_JTQX01000001.1 Protein Homology CDS 0 1160 +
dbxref : GenBank:WP_033973810.1
gbkey : CDS
id : cds-WP_033973810.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009621396.1
locus_tag : NS60_RS00005
name : WP_033973810.1
parent : gene-NS60_RS00005
partial : true
product : ComEC/Rec2 family competence protein
protein_id : WP_033973810.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271913/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQX01000001.1 Protein Homology CDS 1 1161 . + 0 ID=cds-WP_033973810.1;Parent=gene-NS60_RS00005;Dbxref=GenBank:WP_033973810.1;Name=WP_033973810.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_009621396.1;locus_tag=NS60_RS00005;partial=true;product=ComEC/Rec2 family competence protein;protein_id=WP_033973810.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS60_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS60_RS00010' for NZ_JTQX01000001.1 Protein Homology CDS 1233 1868 +
dbxref : GenBank:WP_003091163.1
gbkey : CDS
go_component : plasma membrane|0005886||IEA,membrane|0016020||IEA
go_function : proton channel activity|0015252||IEA
go_process : protein transport|0015031||IEA
id : cds-WP_003091163.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251673.1
locus_tag : NS60_RS00010
name : WP_003091163.1
ontology_term : GO:0015031,GO:0015252,GO:0005886,GO:0016020
parent : gene-NS60_RS00010
product : MotA/TolQ/ExbB proton channel family protein
protein_id : WP_003091163.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271913/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQX01000001.1 Protein Homology CDS 1234 1869 . + 0 ID=cds-WP_003091163.1;Parent=gene-NS60_RS00010;Dbxref=GenBank:WP_003091163.1;Name=WP_003091163.1;Ontology_term=GO:0015031,GO:0015252,GO:0005886,GO:0016020;gbkey=CDS;go_component=plasma membrane|0005886||IEA,membrane|0016020||IEA;go_function=proton channel activity|0015252||IEA;go_process=protein transport|0015031||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251673.1;locus_tag=NS60_RS00010;product=MotA/TolQ/ExbB proton channel family protein;protein_id=WP_003091163.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS60_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS60_RS00015' for NZ_JTQX01000001.1 Protein Homology CDS 1865 2305 +
dbxref : GenBank:WP_003091161.1
gbkey : CDS
go_function : transmembrane transporter activity|0022857||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003091161.1
inference : COO |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271914/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271914/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271914/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271914/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271914/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS62_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS62_RS00005' for NZ_JTQV01000001.1 Protein Homology CDS 30 2486 +
dbxref : GenBank:WP_023114068.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_function : fimbrial usher porin activity|0015473||IEA
go_process : pilus assembly|0009297||IEA
id : cds-WP_023114068.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003448974.1
locus_tag : NS62_RS00005
name : WP_023114068.1
ontology_term : GO:0009297,GO:0015473,GO:0016020
parent : gene-NS62_RS00005
product : fimbria/pilus outer membrane usher protein
protein_id : WP_023114068.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271914/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQV01000001.1 Protein Homology CDS 31 2487 . + 0 ID=cds-WP_023114068.1;Parent=gene-NS62_RS00005;Dbxref=GenBank:WP_023114068.1;Name=WP_023114068.1;Ontology_term=GO:0009297,GO:0015473,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_function=fimbrial usher porin activity|0015473||IEA;go_process=pilus assembly|0009297||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003448974.1;locus_tag=NS62_RS00005;product=fimbria/pilus outer membrane usher protein;protein_id=WP_023114068.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS62_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS62_RS00010' for NZ_JTQV01000001.1 Protein Homology CDS 2566 3087 -
dbxref : GenBank:WP_003086236.1
gbkey : CDS
go_function : DNA binding|0003677||IEA,methylated-DNA-[protein]-cysteine S-methyltransferase activity|0003908||IEA,metal ion binding|0046872||IEA
go_process : DNA repair|0006281||IEA,methylation|0032259||IEA
id : cds-WP_003086236.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249686.1
locus_tag : NS62_RS00010
name : WP_003086236.1
ontology_term : GO:0006281,GO:0032259,GO:0003677,GO:0003908,GO:0046872
parent : gene-NS62_RS00010
product : methylated-DNA--[protein]-cysteine S-methyltransferase
protein_id : WP_003086236.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271914/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQV01000001.1 Protein Homology CDS 2567 3088 . - 0 ID=cds-WP_003086236.1;Parent=gene-NS62_RS00010;Dbxref=GenBank:WP_003086236.1;Name=WP_003086236.1;Ontology_term=GO:0006281,GO:0032259,GO:0003677,GO:0003908,GO:0046872;gbkey=CDS;go_function=DNA binding|0003677||IEA,methylated-DNA-[protein]-cysteine S-methyltransferase activity|0003908||IEA,metal ion binding|0046872||IEA;go_process=DNA repair|0006281||IEA,methylation|0032259||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249686.1;locus_tag=NS62_RS00010;product=methylated-DNA--[protein]-cysteine S-methyltransferase;protein_id=WP_0030 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271915/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271915/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271915/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271915/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271915/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS64_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS64_RS00005' for NZ_JTQT01000001.1 Protein Homology CDS 215 2206 +
dbxref : GenBank:WP_003083920.1
gbkey : CDS
gene : siaA
id : cds-WP_003083920.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248862.1
locus_tag : NS64_RS00005
name : WP_003083920.1
note : SiaB is a threonine kinase acting on SiaC%3B SiaA is the matching phosphatase.
parent : gene-NS64_RS00005
product : biofilm regulation protein phosphatase SiaA
protein_id : WP_003083920.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271915/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQT01000001.1 Protein Homology CDS 216 2207 . + 0 ID=cds-WP_003083920.1;Parent=gene-NS64_RS00005;Dbxref=GenBank:WP_003083920.1;Name=WP_003083920.1;Note=SiaB is a threonine kinase acting on SiaC%3B SiaA is the matching phosphatase.;gbkey=CDS;gene=siaA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248862.1;locus_tag=NS64_RS00005;product=biofilm regulation protein phosphatase SiaA;protein_id=WP_003083920.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS64_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS64_RS00010' for NZ_JTQT01000001.1 Protein Homology CDS 2215 2757 +
dbxref : GenBank:WP_003083916.1
gbkey : CDS
gene : siaB
id : cds-WP_003083916.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248861.1
locus_tag : NS64_RS00010
name : WP_003083916.1
parent : gene-NS64_RS00010
product : biofilm formation regulator kinase SiaB
protein_id : WP_003083916.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271915/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQT01000001.1 Protein Homology CDS 2216 2758 . + 0 ID=cds-WP_003083916.1;Parent=gene-NS64_RS00010;Dbxref=GenBank:WP_003083916.1;Name=WP_003083916.1;gbkey=CDS;gene=siaB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248861.1;locus_tag=NS64_RS00010;product=biofilm formation regulator kinase SiaB;protein_id=WP_003083916.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS64_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS64_RS00015' for NZ_JTQT01000001.1 Protein Homology CDS 2784 3164 +
dbxref : GenBank:WP_003083913.1
gbkey : CDS
gene : siaC
id : cds-WP_003083913.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248860.1
locus_tag : NS64_RS00015
name : WP_003083913.1
parent : gene-NS64_RS00015
product : biofilm formation regulator SiaD modulator protein SiaC
protein_id : WP_003083913.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271915/working/snpeff_out |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271916/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271916/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271916/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271916/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271916/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS65_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS65_RS00005' for NZ_JTQS01000001.1 GeneMarkS-2+ CDS 418 960 +
dbxref : GenBank:WP_003122765.1
gbkey : CDS
id : cds-WP_003122765.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : NS65_RS00005
name : WP_003122765.1
parent : gene-NS65_RS00005
product : hypothetical protein
protein_id : WP_003122765.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271916/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQS01000001.1 GeneMarkS-2+ CDS 419 961 . + 0 ID=cds-WP_003122765.1;Parent=gene-NS65_RS00005;Dbxref=GenBank:WP_003122765.1;Name=WP_003122765.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=NS65_RS00005;product=hypothetical protein;protein_id=WP_003122765.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS65_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS65_RS00010' for NZ_JTQS01000001.1 Protein Homology CDS 983 2182 -
dbxref : GenBank:WP_003089192.1
gbkey : CDS
go_function : DNA binding|0003677||IEA
id : cds-WP_003089192.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_010953724.1
locus_tag : NS65_RS00010
name : WP_003089192.1
ontology_term : GO:0003677
parent : gene-NS65_RS00010
product : PucR family transcriptional regulator
protein_id : WP_003089192.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271916/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQS01000001.1 Protein Homology CDS 984 2183 . - 0 ID=cds-WP_003089192.1;Parent=gene-NS65_RS00010;Dbxref=GenBank:WP_003089192.1;Name=WP_003089192.1;Ontology_term=GO:0003677;gbkey=CDS;go_function=DNA binding|0003677||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_010953724.1;locus_tag=NS65_RS00010;product=PucR family transcriptional regulator;protein_id=WP_003089192.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS65_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS65_RS00015' for NZ_JTQS01000001.1 Protein Homology CDS 2476 3342 +
dbxref : GenBank:WP_003089190.1
gbkey : CDS
go_function : metal ion binding|0046872||IEA,dioxygenase activity|0051213||IEA
id : cds-WP_003089190.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003144174.1
locus_tag : NS65_RS00015
name : WP_003089190.1
ontology_term : GO:0046872,GO:0051213
parent : gene-NS65_RS00015
product : phytanoyl-CoA dioxygenase family protein
protein_id : WP_003089190.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271916/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQS01000001.1 Protein Homology CDS 2477 3343 . + 0 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271917/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271917/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271917/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271917/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271917/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS66_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS66_RS00005' for NZ_JTQR01000001.1 Protein Homology CDS 286 4143 +
dbxref : GenBank:WP_408980346.1
gbkey : CDS
id : cds-WP_408980346.1
inference : COORDINATES: protein motif:HMM:NF012873.6
locus_tag : NS66_RS00005
name : WP_408980346.1
parent : gene-NS66_RS00005
product : amino acid adenylation domain-containing protein
protein_id : WP_408980346.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271917/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQR01000001.1 Protein Homology CDS 287 4144 . + 0 ID=cds-WP_408980346.1;Parent=gene-NS66_RS00005;Dbxref=GenBank:WP_408980346.1;Name=WP_408980346.1;gbkey=CDS;inference=COORDINATES: protein motif:HMM:NF012873.6;locus_tag=NS66_RS00005;product=amino acid adenylation domain-containing protein;protein_id=WP_408980346.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS66_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS66_RS00010' for NZ_JTQR01000001.1 Protein Homology CDS 4192 5157 +
dbxref : GenBank:WP_003122673.1
gbkey : CDS
go_function : hydrolase activity|0016787||IEA
id : cds-WP_003122673.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003122673.1
locus_tag : NS66_RS00010
name : WP_003122673.1
ontology_term : GO:0016787
parent : gene-NS66_RS00010
product : alpha/beta hydrolase
protein_id : WP_003122673.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271917/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQR01000001.1 Protein Homology CDS 4193 5158 . + 0 ID=cds-WP_003122673.1;Parent=gene-NS66_RS00010;Dbxref=GenBank:WP_003122673.1;Name=WP_003122673.1;Ontology_term=GO:0016787;gbkey=CDS;go_function=hydrolase activity|0016787||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003122673.1;locus_tag=NS66_RS00010;product=alpha/beta hydrolase;protein_id=WP_003122673.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS66_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS66_RS00015' for NZ_JTQR01000001.1 Protein Homology CDS 5258 7684 -
dbxref : GenBank:WP_003144001.1
gbkey : CDS
go_function : channel activity|0015267||IEA,siderophore-iron transmembrane transporter activity|0015343||IEA,metal ion binding|0046872||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_003144001.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_012075666.1
locus_tag : NS66_RS00015
name : WP_003144001.1
ontology_term : GO:0055085,GO:0015267,GO:0015343,GO:0046872
parent : gene-NS66_RS00015
product : TonB-dependent siderophore receptor
protein_id : WP_003144001.1
source : Protein Homology
transl_table : 11
type |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271918/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271918/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271918/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271918/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271918/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS67_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS67_RS00005' for NZ_JTQQ01000001.1 GeneMarkS-2+ CDS 220 522 +
dbxref : GenBank:WP_015648585.1
gbkey : CDS
id : cds-WP_015648585.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : NS67_RS00005
name : WP_015648585.1
parent : gene-NS67_RS00005
product : hypothetical protein
protein_id : WP_015648585.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271918/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQQ01000001.1 GeneMarkS-2+ CDS 221 523 . + 0 ID=cds-WP_015648585.1;Parent=gene-NS67_RS00005;Dbxref=GenBank:WP_015648585.1;Name=WP_015648585.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=NS67_RS00005;product=hypothetical protein;protein_id=WP_015648585.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS67_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS67_RS00010' for NZ_JTQQ01000001.1 Protein Homology CDS 533 739 +
dbxref : GenBank:WP_003159008.1
gbkey : CDS
id : cds-WP_003159008.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003159008.1
locus_tag : NS67_RS00010
name : WP_003159008.1
parent : gene-NS67_RS00010
product : hypothetical protein
protein_id : WP_003159008.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271918/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQQ01000001.1 Protein Homology CDS 534 740 . + 0 ID=cds-WP_003159008.1;Parent=gene-NS67_RS00010;Dbxref=GenBank:WP_003159008.1;Name=WP_003159008.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003159008.1;locus_tag=NS67_RS00010;product=hypothetical protein;protein_id=WP_003159008.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS67_RS33920' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS67_RS33920' for NZ_JTQQ01000001.1 GeneMarkS-2+ CDS 978 1136 +
dbxref : GenBank:WP_153574150.1
gbkey : CDS
id : cds-WP_153574150.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : NS67_RS33920
name : WP_153574150.1
parent : gene-NS67_RS33920
product : hypothetical protein
protein_id : WP_153574150.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271918/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQQ01000001.1 GeneMarkS-2+ CDS 979 1137 . + 0 ID=cds-WP_153574150.1;Parent=gene-NS67_RS33920;Dbxref=GenBank:WP_153574150.1;Name=WP_153574150.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=NS67_RS33920;product=hypothetical protein;protein_id=WP_153574150.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS67_RS00025' is a Gene instead |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271919/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271919/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271919/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271919/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271919/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS68_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS68_RS00005' for NZ_JTQP01000001.1 Protein Homology CDS 0 372 -
dbxref : GenBank:WP_033980509.1
gbkey : CDS
go_function : protein serine/threonine phosphatase activity|0004722||IEA,metal ion binding|0046872||IEA
go_process : protein dephosphorylation|0006470||IEA
id : cds-WP_033980509.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250361.1
locus_tag : NS68_RS00005
name : WP_033980509.1
ontology_term : GO:0006470,GO:0004722,GO:0046872
parent : gene-NS68_RS00005
partial : true
product : PP2C family protein-serine/threonine phosphatase
protein_id : WP_033980509.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271919/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQP01000001.1 Protein Homology CDS 1 373 . - 0 ID=cds-WP_033980509.1;Parent=gene-NS68_RS00005;Dbxref=GenBank:WP_033980509.1;Name=WP_033980509.1;Ontology_term=GO:0006470,GO:0004722,GO:0046872;gbkey=CDS;go_function=protein serine/threonine phosphatase activity|0004722||IEA,metal ion binding|0046872||IEA;go_process=protein dephosphorylation|0006470||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250361.1;locus_tag=NS68_RS00005;partial=true;product=PP2C family protein-serine/threonine phosphatase;protein_id=WP_033980509.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS68_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS68_RS00010' for NZ_JTQP01000001.1 Protein Homology CDS 372 3899 -
dbxref : GenBank:WP_033980511.1
gbkey : CDS
gene : tssM
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_033980511.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250360.1
locus_tag : NS68_RS00010
name : WP_033980511.1
ontology_term : GO:0033103
parent : gene-NS68_RS00010
product : type VI secretion system membrane subunit TssM
protein_id : WP_033980511.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271919/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQP01000001.1 Protein Homology CDS 373 3900 . - 0 ID=cds-WP_033980511.1;Parent=gene-NS68_RS00010;Dbxref=GenBank:WP_033980511.1;Name=WP_033980511.1;Ontology_term=GO:0033103;gbkey=CDS;gene=tssM;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250360.1;locus_tag=NS68_RS00010;product=type VI secretion system membrane subunit TssM;protein_id=WP_033980511.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS68_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS68_RS00015' for NZ_JTQP01000001.1 Protein H |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271920/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271920/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271920/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271920/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271920/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS69_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS69_RS00005' for NZ_JTQO01000001.1 Protein Homology CDS 17 772 +
dbxref : GenBank:WP_016851742.1
gbkey : CDS
gene : modA
go_component : outer membrane-bounded periplasmic space|0030288||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ABC-type molybdate transporter activity|0015412||IEA,molybdate ion binding|0030973||IEA
go_process : molybdate ion transport|0015689||IEA
id : cds-WP_016851742.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250554.1
locus_tag : NS69_RS00005
name : WP_016851742.1
ontology_term : GO:0015689,GO:0015412,GO:0030973,GO:0030288,GO:0055052
parent : gene-NS69_RS00005
product : molybdate ABC transporter substrate-binding protein
protein_id : WP_016851742.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271920/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQO01000001.1 Protein Homology CDS 18 773 . + 0 ID=cds-WP_016851742.1;Parent=gene-NS69_RS00005;Dbxref=GenBank:WP_016851742.1;Name=WP_016851742.1;Ontology_term=GO:0015689,GO:0015412,GO:0030973,GO:0030288,GO:0055052;gbkey=CDS;gene=modA;go_component=outer membrane-bounded periplasmic space|0030288||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA;go_function=ABC-type molybdate transporter activity|0015412||IEA,molybdate ion binding|0030973||IEA;go_process=molybdate ion transport|0015689||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250554.1;locus_tag=NS69_RS00005;product=molybdate ABC transporter substrate-binding protein;protein_id=WP_016851742.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS69_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS69_RS00010' for NZ_JTQO01000001.1 Protein Homology CDS 785 1471 +
dbxref : GenBank:WP_003088068.1
gbkey : CDS
gene : modB
go_component : plasma membrane|0005886||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ABC-type molybdate transporter activity|0015412||IEA
go_process : molybdate ion transport|0015689||IEA
id : cds-WP_003088068.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250553.1
locus_tag : NS69_RS00010
name : WP_003088068.1
ontology_term : GO:0015689,GO:0015412,GO:0005886,GO:0055052
parent : gene-NS69_RS00010
product : molybdate ABC transporter permease subunit
protein_id : WP_003088068.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271920/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQO01000001.1 Protein Homology CDS 786 1472 . + 0 ID=cds-WP_003088068.1;Parent=g |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271921/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271921/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271921/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271921/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271921/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS71_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS71_RS00005' for NZ_JTQM01000001.1 Protein Homology CDS 14 466 +
dbxref : GenBank:WP_003095076.1
gbkey : CDS
id : cds-WP_003095076.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253385.1
locus_tag : NS71_RS00005
name : WP_003095076.1
parent : gene-NS71_RS00005
product : DUF4124 domain-containing protein
protein_id : WP_003095076.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271921/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQM01000001.1 Protein Homology CDS 15 467 . + 0 ID=cds-WP_003095076.1;Parent=gene-NS71_RS00005;Dbxref=GenBank:WP_003095076.1;Name=WP_003095076.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253385.1;locus_tag=NS71_RS00005;product=DUF4124 domain-containing protein;protein_id=WP_003095076.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS71_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS71_RS00010' for NZ_JTQM01000001.1 Protein Homology CDS 574 903 -
dbxref : GenBank:WP_003123490.1
gbkey : CDS
id : cds-WP_003123490.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253386.1
locus_tag : NS71_RS00010
name : WP_003123490.1
parent : gene-NS71_RS00010
product : YqcC family protein
protein_id : WP_003123490.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271921/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQM01000001.1 Protein Homology CDS 575 904 . - 0 ID=cds-WP_003123490.1;Parent=gene-NS71_RS00010;Dbxref=GenBank:WP_003123490.1;Name=WP_003123490.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253386.1;locus_tag=NS71_RS00010;product=YqcC family protein;protein_id=WP_003123490.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS71_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS71_RS00015' for NZ_JTQM01000001.1 Protein Homology CDS 903 1682 -
dbxref : GenBank:WP_003123491.1
gbkey : CDS
gene : lpoP
id : cds-WP_003123491.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253387.1
locus_tag : NS71_RS00015
name : WP_003123491.1
parent : gene-NS71_RS00015
product : penicillin-binding protein activator LpoP
protein_id : WP_003123491.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271921/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQM01000001.1 Protein Homology CDS 904 1683 . - 0 ID=cds-WP_003123491.1;Parent=gene-NS71_RS00015;Dbxref=GenBank:WP_003123491.1;Name=WP_003123491.1;gbkey=CDS;gene=lpoP;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253387.1;locus_tag=NS71_RS00015;product=penicillin-binding p |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271922/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271922/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271922/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271922/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271922/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS73_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS73_RS00005' for NZ_JTQK01000001.1 Protein Homology CDS 319 1175 -
dbxref : GenBank:WP_043547750.1
gbkey : CDS
go_function : ATP binding|0005524||IEA,transcription factor binding|0008134||IEA
go_process : regulation of DNA-templated transcription|0006355||IEA
id : cds-WP_043547750.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252621.1
locus_tag : NS73_RS00005
name : WP_043547750.1
ontology_term : GO:0006355,GO:0005524,GO:0008134
parent : gene-NS73_RS00005
partial : true
product : sigma 54-interacting transcriptional regulator
protein_id : WP_043547750.1
source : Protein Homology
start_range : .,320
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271922/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQK01000001.1 Protein Homology CDS 320 1176 . - 0 ID=cds-WP_043547750.1;Parent=gene-NS73_RS00005;Dbxref=GenBank:WP_043547750.1;Name=WP_043547750.1;Ontology_term=GO:0006355,GO:0005524,GO:0008134;gbkey=CDS;go_function=ATP binding|0005524||IEA,transcription factor binding|0008134||IEA;go_process=regulation of DNA-templated transcription|0006355||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252621.1;locus_tag=NS73_RS00005;partial=true;product=sigma 54-interacting transcriptional regulator;protein_id=WP_043547750.1;start_range=.,320;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS73_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS73_RS00010' for NZ_JTQK01000001.1 Protein Homology CDS 1350 2129 -
dbxref : GenBank:WP_003093057.1
gbkey : CDS
go_component : plasma membrane|0005886||IEA
go_function : ATPase-coupled transmembrane transporter activity|0042626||IEA,ABC-type transporter activity|0140359||IEA
id : cds-WP_003093057.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252620.1
locus_tag : NS73_RS00010
name : WP_003093057.1
ontology_term : GO:0042626,GO:0140359,GO:0005886
parent : gene-NS73_RS00010
product : MetQ/NlpA family ABC transporter substrate-binding protein
protein_id : WP_003093057.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271922/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQK01000001.1 Protein Homology CDS 1351 2130 . - 0 ID=cds-WP_003093057.1;Parent=gene-NS73_RS00010;Dbxref=GenBank:WP_003093057.1;Name=WP_003093057.1;Ontology_term=GO:0042626,GO:0140359,GO:0005886;gbkey=CDS;go_component=plasma membrane|0005886||IEA;go_function=ATPase-coupled transmembrane transporter activity|0042626||IEA,ABC-type transporter activity|0140359||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252620.1;locus_tag=NS73_RS00010;product=MetQ/NlpA family ABC transporter substrate-binding protein;protein_id=WP_003093057.1;tra |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271923/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271923/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271923/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271923/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271923/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS70_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS70_RS00005' for NZ_JTQN01000001.1 Protein Homology CDS 0 231 +
dbxref : GenBank:WP_033877954.1
gbkey : CDS
go_function : oxidoreductase activity|0016491||IEA
id : cds-WP_033877954.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250674.1
locus_tag : NS70_RS00005
name : WP_033877954.1
ontology_term : GO:0016491
parent : gene-NS70_RS00005
partial : true
product : aldehyde dehydrogenase family protein
protein_id : WP_033877954.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271923/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQN01000001.1 Protein Homology CDS 1 232 . + 1 ID=cds-WP_033877954.1;Parent=gene-NS70_RS00005;Dbxref=GenBank:WP_033877954.1;Name=WP_033877954.1;Ontology_term=GO:0016491;gbkey=CDS;go_function=oxidoreductase activity|0016491||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250674.1;locus_tag=NS70_RS00005;partial=true;product=aldehyde dehydrogenase family protein;protein_id=WP_033877954.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS70_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS70_RS00010' for NZ_JTQN01000001.1 Protein Homology CDS 441 1889 +
dbxref : GenBank:WP_003093230.1
gbkey : CDS
gene : eat
go_component : membrane|0016020||IEA
go_function : amino acid transmembrane transporter activity|0015171||IEA
go_process : amino acid transport|0006865||IEA
id : cds-WP_003093230.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252712.1
locus_tag : NS70_RS00010
name : WP_003093230.1
ontology_term : GO:0006865,GO:0015171,GO:0016020
parent : gene-NS70_RS00010
product : ethanolamine permease
protein_id : WP_003093230.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271923/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQN01000001.1 Protein Homology CDS 442 1890 . + 0 ID=cds-WP_003093230.1;Parent=gene-NS70_RS00010;Dbxref=GenBank:WP_003093230.1;Name=WP_003093230.1;Ontology_term=GO:0006865,GO:0015171,GO:0016020;gbkey=CDS;gene=eat;go_component=membrane|0016020||IEA;go_function=amino acid transmembrane transporter activity|0015171||IEA;go_process=amino acid transport|0006865||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252712.1;locus_tag=NS70_RS00010;product=ethanolamine permease;protein_id=WP_003093230.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS70_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS70_RS00015' for NZ_JTQN01000001.1 Protein Homology CDS 1947 3341 +
dbxref : GenBank:WP_003093232.1
gbkey : CDS
id : cds-WP_003093232.1
inference : COORDINATES: similar to |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271924/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271924/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271924/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271924/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271924/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS74_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS74_RS00005' for NZ_JTQJ01000001.1 Protein Homology CDS 0 1152 +
dbxref : GenBank:WP_033938284.1
gbkey : CDS
gene : hemW
go_component : cytoplasm|0005737||IEA
go_function : 4 iron%2C 4 sulfur cluster binding|0051539||IEA,coproporphyrinogen dehydrogenase activity|0051989||IEA
go_process : porphyrin-containing compound biosynthetic process|0006779||IEA
id : cds-WP_033938284.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249077.1
locus_tag : NS74_RS00005
name : WP_033938284.1
ontology_term : GO:0006779,GO:0051539,GO:0051989,GO:0005737
parent : gene-NS74_RS00005
partial : true
product : radical SAM family heme chaperone HemW
protein_id : WP_033938284.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271924/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQJ01000001.1 Protein Homology CDS 1 1153 . + 1 ID=cds-WP_033938284.1;Parent=gene-NS74_RS00005;Dbxref=GenBank:WP_033938284.1;Name=WP_033938284.1;Ontology_term=GO:0006779,GO:0051539,GO:0051989,GO:0005737;gbkey=CDS;gene=hemW;go_component=cytoplasm|0005737||IEA;go_function=4 iron%2C 4 sulfur cluster binding|0051539||IEA,coproporphyrinogen dehydrogenase activity|0051989||IEA;go_process=porphyrin-containing compound biosynthetic process|0006779||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249077.1;locus_tag=NS74_RS00005;partial=true;product=radical SAM family heme chaperone HemW;protein_id=WP_033938284.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS74_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS74_RS00010' for NZ_JTQJ01000001.1 Protein Homology CDS 1233 1556 +
dbxref : GenBank:WP_003084525.1
gbkey : CDS
id : cds-WP_003084525.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249076.1
locus_tag : NS74_RS00010
name : WP_003084525.1
parent : gene-NS74_RS00010
product : DUF3392 domain-containing protein
protein_id : WP_003084525.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271924/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQJ01000001.1 Protein Homology CDS 1234 1557 . + 0 ID=cds-WP_003084525.1;Parent=gene-NS74_RS00010;Dbxref=GenBank:WP_003084525.1;Name=WP_003084525.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249076.1;locus_tag=NS74_RS00010;product=DUF3392 domain-containing protein;protein_id=WP_003084525.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS74_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS74_RS00015' for NZ_JTQJ01000001.1 Protein Homology CDS 1618 1875 +
dbxref : GenBank:WP_003084524.1
gbkey : CDS
id : cds |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271925/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271925/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271925/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271925/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271925/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS75_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS75_RS00005' for NZ_JTQI01000001.1 Protein Homology CDS 265 1077 +
dbxref : GenBank:WP_033988618.1
gbkey : CDS
id : cds-WP_033988618.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003050359.1
locus_tag : NS75_RS00005
name : WP_033988618.1
parent : gene-NS75_RS00005
product : hypothetical protein
protein_id : WP_033988618.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271925/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQI01000001.1 Protein Homology CDS 266 1078 . + 0 ID=cds-WP_033988618.1;Parent=gene-NS75_RS00005;Dbxref=GenBank:WP_033988618.1;Name=WP_033988618.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003050359.1;locus_tag=NS75_RS00005;product=hypothetical protein;protein_id=WP_033988618.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS75_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS75_RS00010' for NZ_JTQI01000001.1 Protein Homology CDS 1487 2392 +
dbxref : GenBank:WP_033988620.1
gbkey : CDS
id : cds-WP_033988620.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003050351.1
locus_tag : NS75_RS00010
name : WP_033988620.1
parent : gene-NS75_RS00010
product : DUF3577 domain-containing protein
protein_id : WP_033988620.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271925/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQI01000001.1 Protein Homology CDS 1488 2393 . + 0 ID=cds-WP_033988620.1;Parent=gene-NS75_RS00010;Dbxref=GenBank:WP_033988620.1;Name=WP_033988620.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003050351.1;locus_tag=NS75_RS00010;product=DUF3577 domain-containing protein;protein_id=WP_033988620.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS75_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS75_RS00015' for NZ_JTQI01000001.1 Protein Homology CDS 2537 3364 +
dbxref : GenBank:WP_033988623.1
gbkey : CDS
id : cds-WP_033988623.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_011871441.1
locus_tag : NS75_RS00015
name : WP_033988623.1
parent : gene-NS75_RS00015
product : DUF932 domain-containing protein
protein_id : WP_033988623.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271925/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQI01000001.1 Protein Homology CDS 2538 3365 . + 0 ID=cds-WP_033988623.1;Parent=gene-NS75_RS00015;Dbxref=GenBank:WP_033988623.1;Name=WP_033988623.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_011871441.1;locus_tag=NS75_RS00015;product=DUF932 domain-containing p |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271926/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271926/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271926/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271926/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271926/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS76_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS76_RS00005' for NZ_JTQH01000001.1 Protein Homology CDS 59 937 +
dbxref : GenBank:WP_003111119.1
gbkey : CDS
gene : aguB
go_component : cytoplasm|0005737||IEA
go_function : N-carbamoylputrescine amidase activity|0050126||IEA
go_process : putrescine biosynthetic process|0009446||IEA
id : cds-WP_003111119.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248984.1
locus_tag : NS76_RS00005
name : WP_003111119.1
ontology_term : GO:0009446,GO:0050126,GO:0005737
parent : gene-NS76_RS00005
product : N-carbamoylputrescine amidase
protein_id : WP_003111119.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271926/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQH01000001.1 Protein Homology CDS 60 938 . + 0 ID=cds-WP_003111119.1;Parent=gene-NS76_RS00005;Dbxref=GenBank:WP_003111119.1;Name=WP_003111119.1;Ontology_term=GO:0009446,GO:0050126,GO:0005737;gbkey=CDS;gene=aguB;go_component=cytoplasm|0005737||IEA;go_function=N-carbamoylputrescine amidase activity|0050126||IEA;go_process=putrescine biosynthetic process|0009446||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248984.1;locus_tag=NS76_RS00005;product=N-carbamoylputrescine amidase;protein_id=WP_003111119.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS76_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS76_RS00010' for NZ_JTQH01000001.1 Protein Homology CDS 1023 2129 +
dbxref : GenBank:WP_023126883.1
gbkey : CDS
gene : aguA
go_component : cytoplasm|0005737||IEA
go_function : agmatine deiminase activity|0047632||IEA
go_process : putrescine biosynthetic process|0009446||IEA
id : cds-WP_023126883.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_248983.1
locus_tag : NS76_RS00010
name : WP_023126883.1
ontology_term : GO:0009446,GO:0047632,GO:0005737
parent : gene-NS76_RS00010
product : agmatine deiminase
protein_id : WP_023126883.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271926/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQH01000001.1 Protein Homology CDS 1024 2130 . + 0 ID=cds-WP_023126883.1;Parent=gene-NS76_RS00010;Dbxref=GenBank:WP_023126883.1;Name=WP_023126883.1;Ontology_term=GO:0009446,GO:0047632,GO:0005737;gbkey=CDS;gene=aguA;go_component=cytoplasm|0005737||IEA;go_function=agmatine deiminase activity|0047632||IEA;go_process=putrescine biosynthetic process|0009446||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_248983.1;locus_tag=NS76_RS00010;product=agmatine deiminase;protein_id=WP_023126883.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS76_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_g |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271927/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271927/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271927/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271927/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271927/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS78_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS78_RS00005' for NZ_JTQF01000001.1 Protein Homology CDS 0 160 +
dbxref : GenBank:WP_033945106.1
gbkey : CDS
go_function : nucleic acid binding|0003676||IEA
id : cds-WP_033945106.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251312.1
locus_tag : NS78_RS00005
name : WP_033945106.1
ontology_term : GO:0003676
parent : gene-NS78_RS00005
partial : true
product : cold-shock protein
protein_id : WP_033945106.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271927/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQF01000001.1 Protein Homology CDS 1 161 . + 2 ID=cds-WP_033945106.1;Parent=gene-NS78_RS00005;Dbxref=GenBank:WP_033945106.1;Name=WP_033945106.1;Ontology_term=GO:0003676;gbkey=CDS;go_function=nucleic acid binding|0003676||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251312.1;locus_tag=NS78_RS00005;partial=true;product=cold-shock protein;protein_id=WP_033945106.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS78_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS78_RS00010' for NZ_JTQF01000001.1 Protein Homology CDS 234 1490 -
dbxref : GenBank:WP_003090436.1
gbkey : CDS
gene : icd
go_function : magnesium ion binding|0000287||IEA,isocitrate dehydrogenase (NADP+) activity|0004450||IEA,NAD binding|0051287||IEA
go_process : tricarboxylic acid cycle|0006099||IEA
id : cds-WP_003090436.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251313.1
locus_tag : NS78_RS00010
name : WP_003090436.1
ontology_term : GO:0006099,GO:0000287,GO:0004450,GO:0051287
parent : gene-NS78_RS00010
product : NADP-dependent isocitrate dehydrogenase
protein_id : WP_003090436.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271927/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQF01000001.1 Protein Homology CDS 235 1491 . - 0 ID=cds-WP_003090436.1;Parent=gene-NS78_RS00010;Dbxref=GenBank:WP_003090436.1;Name=WP_003090436.1;Ontology_term=GO:0006099,GO:0000287,GO:0004450,GO:0051287;gbkey=CDS;gene=icd;go_function=magnesium ion binding|0000287||IEA,isocitrate dehydrogenase (NADP+) activity|0004450||IEA,NAD binding|0051287||IEA;go_process=tricarboxylic acid cycle|0006099||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_251313.1;locus_tag=NS78_RS00010;product=NADP-dependent isocitrate dehydrogenase;protein_id=WP_003090436.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS78_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS78_RS00015' for NZ_JTQF01000001.1 Protein Homology CDS 1849 4074 +
dbxref : GenBank:WP_003090437.1
gbkey : CDS
go_fu |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271928/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271928/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271928/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271928/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271928/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS79_RS08830' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS79_RS08830' for NZ_JTQE01000010.1 Protein Homology CDS 296 1525 +
dbxref : GenBank:WP_003107018.1
gbkey : CDS
id : cds-WP_003107018.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252971.1
locus_tag : NS79_RS08830
name : WP_003107018.1
parent : gene-NS79_RS08830
product : exonuclease SbcCD subunit D C-terminal domain-containing protein
protein_id : WP_003107018.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271928/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQE01000010.1 Protein Homology CDS 297 1526 . + 0 ID=cds-WP_003107018.1;Parent=gene-NS79_RS08830;Dbxref=GenBank:WP_003107018.1;Name=WP_003107018.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252971.1;locus_tag=NS79_RS08830;product=exonuclease SbcCD subunit D C-terminal domain-containing protein;protein_id=WP_003107018.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS79_RS08835' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS79_RS08835' for NZ_JTQE01000010.1 Protein Homology CDS 1534 5169 +
dbxref : GenBank:WP_033993895.1
gbkey : CDS
go_function : ATP hydrolysis activity|0016887||IEA
go_process : double-strand break repair|0006302||IEA
id : cds-WP_033993895.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_008569778.1
locus_tag : NS79_RS08835
name : WP_033993895.1
ontology_term : GO:0006302,GO:0016887
parent : gene-NS79_RS08835
product : AAA family ATPase
protein_id : WP_033993895.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271928/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQE01000010.1 Protein Homology CDS 1535 5170 . + 0 ID=cds-WP_033993895.1;Parent=gene-NS79_RS08835;Dbxref=GenBank:WP_033993895.1;Name=WP_033993895.1;Ontology_term=GO:0006302,GO:0016887;gbkey=CDS;go_function=ATP hydrolysis activity|0016887||IEA;go_process=double-strand break repair|0006302||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_008569778.1;locus_tag=NS79_RS08835;product=AAA family ATPase;protein_id=WP_033993895.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS79_RS08840' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS79_RS08840' for NZ_JTQE01000010.1 Protein Homology CDS 5191 7356 -
dbxref : GenBank:WP_023113536.1
gbkey : CDS
gene : recD
go_component : exodeoxyribonuclease V complex|0009338||IEA
go_function : helicase activity|0004386||IEA,exodeoxyribonuclease V activity|0008854||IEA
go_process : DNA repair|0006281||IEA,DNA recombination|0006310||IEA
id : cds-WP_023113536.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252973.1
locus_tag : NS79_RS08840
name : |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271929/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271929/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271929/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271929/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271929/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS80_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS80_RS00010' for NZ_JTQD01000001.1 Protein Homology CDS 347 2422 +
dbxref : GenBank:WP_003457827.1
gbkey : CDS
go_component : type VI protein secretion system complex|0033104||IEA
go_process : protein secretion by the type VI secretion system|0033103||IEA
id : cds-WP_003457827.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_253953.1
locus_tag : NS80_RS00010
name : WP_003457827.1
ontology_term : GO:0033103,GO:0033104
parent : gene-NS80_RS00010
product : type VI secretion system tip protein VgrG
protein_id : WP_003457827.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271929/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQD01000001.1 Protein Homology CDS 348 2423 . + 0 ID=cds-WP_003457827.1;Parent=gene-NS80_RS00010;Dbxref=GenBank:WP_003457827.1;Name=WP_003457827.1;Ontology_term=GO:0033103,GO:0033104;gbkey=CDS;go_component=type VI protein secretion system complex|0033104||IEA;go_process=protein secretion by the type VI secretion system|0033103||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_253953.1;locus_tag=NS80_RS00010;product=type VI secretion system tip protein VgrG;protein_id=WP_003457827.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS80_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS80_RS00015' for NZ_JTQD01000001.1 GeneMarkS-2+ CDS 2419 5688 +
dbxref : GenBank:WP_023083278.1
gbkey : CDS
id : cds-WP_023083278.1
inference : COORDINATES: ab initio prediction:GeneMarkS-2+
locus_tag : NS80_RS00015
name : WP_023083278.1
parent : gene-NS80_RS00015
product : hypothetical protein
protein_id : WP_023083278.1
source : GeneMarkS-2+
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271929/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTQD01000001.1 GeneMarkS-2+ CDS 2420 5689 . + 0 ID=cds-WP_023083278.1;Parent=gene-NS80_RS00015;Dbxref=GenBank:WP_023083278.1;Name=WP_023083278.1;gbkey=CDS;inference=COORDINATES: ab initio prediction:GeneMarkS-2+;locus_tag=NS80_RS00015;product=hypothetical protein;protein_id=WP_023083278.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS80_RS35470' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS80_RS35470' for NZ_JTQD01000001.1 Protein Homology CDS 6267 6890 +
dbxref : GenBank:WP_031299557.1
gbkey : CDS
id : cds-WP_031299557.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003099240.1
locus_tag : NS80_RS35470
name : WP_031299557.1
parent : gene-NS80_RS35470
product : hypothetical protein
protein_id : WP_031299557.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271929/w |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271930/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271930/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271930/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271930/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271930/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS88_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS88_RS00005' for NZ_JTPV01000001.1 Protein Homology CDS 0 1273 +
dbxref : GenBank:WP_033961367.1
gbkey : CDS
go_function : hydrolase activity|0016787||IEA
id : cds-WP_033961367.1
inference : COORDINATES: protein motif:HMM:NF012958.6
locus_tag : NS88_RS00005
name : WP_033961367.1
ontology_term : GO:0016787
parent : gene-NS88_RS00005
partial : true
product : alpha/beta hydrolase
protein_id : WP_033961367.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271930/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPV01000001.1 Protein Homology CDS 1 1274 . + 2 ID=cds-WP_033961367.1;Parent=gene-NS88_RS00005;Dbxref=GenBank:WP_033961367.1;Name=WP_033961367.1;Ontology_term=GO:0016787;gbkey=CDS;go_function=hydrolase activity|0016787||IEA;inference=COORDINATES: protein motif:HMM:NF012958.6;locus_tag=NS88_RS00005;partial=true;product=alpha/beta hydrolase;protein_id=WP_033961367.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS88_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS88_RS00010' for NZ_JTPV01000001.1 Protein Homology CDS 1476 2393 +
dbxref : GenBank:WP_003122400.1
gbkey : CDS
id : cds-WP_003122400.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_015648892.1
locus_tag : NS88_RS00010
name : WP_003122400.1
parent : gene-NS88_RS00010
product : hypothetical protein
protein_id : WP_003122400.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271930/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPV01000001.1 Protein Homology CDS 1477 2394 . + 0 ID=cds-WP_003122400.1;Parent=gene-NS88_RS00010;Dbxref=GenBank:WP_003122400.1;Name=WP_003122400.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:WP_015648892.1;locus_tag=NS88_RS00010;product=hypothetical protein;protein_id=WP_003122400.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS88_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS88_RS00015' for NZ_JTPV01000001.1 Protein Homology CDS 2475 4010 +
dbxref : GenBank:WP_003105794.1
gbkey : CDS
id : cds-WP_003105794.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_251139.1
locus_tag : NS88_RS00015
name : WP_003105794.1
parent : gene-NS88_RS00015
product : sigma-54-dependent transcriptional regulator
protein_id : WP_003105794.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271930/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTPV01000001.1 Protein Homology CDS 2476 4011 . + 0 ID=cds-WP_003105794.1;Parent=gene-NS88_RS00015;Dbxref=GenBank:WP_003105794.1;Na |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271931/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271931/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271931/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271931/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271931/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS87_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS87_RS00005' for NZ_JTPW01000001.1 Protein Homology CDS 41 1819 -
dbxref : GenBank:WP_015502251.1
gbkey : CDS
id : cds-WP_015502251.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249199.1
locus_tag : NS87_RS00005
name : WP_015502251.1
parent : gene-NS87_RS00005
product : acyl-CoA dehydrogenase C-terminal domain-containing protein
protein_id : WP_015502251.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271931/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPW01000001.1 Protein Homology CDS 42 1820 . - 0 ID=cds-WP_015502251.1;Parent=gene-NS87_RS00005;Dbxref=GenBank:WP_015502251.1;Name=WP_015502251.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249199.1;locus_tag=NS87_RS00005;product=acyl-CoA dehydrogenase C-terminal domain-containing protein;protein_id=WP_015502251.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS87_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS87_RS00010' for NZ_JTPW01000001.1 Protein Homology CDS 2094 3890 -
dbxref : GenBank:WP_003111242.1
gbkey : CDS
id : cds-WP_003111242.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249198.1
locus_tag : NS87_RS00010
name : WP_003111242.1
parent : gene-NS87_RS00010
product : acyl-CoA dehydrogenase C-terminal domain-containing protein
protein_id : WP_003111242.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271931/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPW01000001.1 Protein Homology CDS 2095 3891 . - 0 ID=cds-WP_003111242.1;Parent=gene-NS87_RS00010;Dbxref=GenBank:WP_003111242.1;Name=WP_003111242.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249198.1;locus_tag=NS87_RS00010;product=acyl-CoA dehydrogenase C-terminal domain-containing protein;protein_id=WP_003111242.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS87_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS87_RS00015' for NZ_JTPW01000001.1 Protein Homology CDS 4103 5908 -
dbxref : GenBank:WP_003084842.1
gbkey : CDS
id : cds-WP_003084842.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249197.1
locus_tag : NS87_RS00015
name : WP_003084842.1
parent : gene-NS87_RS00015
product : phenylacyl-CoA dehydrogenase
protein_id : WP_003084842.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271931/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_JTPW01000001.1 Protein Homology CDS 4104 5909 . - 0 ID=cds-WP_003084842.1;Parent=gene-NS87_RS00015;Dbxref=GenBank:WP_003084842.1;Name=WP_003084842.1;gbkey=CDS;inference=COO |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271932/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271932/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271932/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271932/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271932/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS86_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS86_RS00005' for NZ_JTPX01000001.1 Protein Homology CDS 350 1321 +
dbxref : GenBank:WP_003096673.1
gbkey : CDS
gene : pstS
id : cds-WP_003096673.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254056.1
locus_tag : NS86_RS00005
name : WP_003096673.1
parent : gene-NS86_RS00005
product : phosphate ABC transporter substrate-binding protein PstS
protein_id : WP_003096673.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271932/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTPX01000001.1 Protein Homology CDS 351 1322 . + 0 ID=cds-WP_003096673.1;Parent=gene-NS86_RS00005;Dbxref=GenBank:WP_003096673.1;Name=WP_003096673.1;gbkey=CDS;gene=pstS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254056.1;locus_tag=NS86_RS00005;product=phosphate ABC transporter substrate-binding protein PstS;protein_id=WP_003096673.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS86_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS86_RS00010' for NZ_JTPX01000001.1 Protein Homology CDS 1744 3777 +
dbxref : GenBank:WP_078451435.1
gbkey : CDS
go_component : membrane|0016020||IEA
go_process : transmembrane transport|0055085||IEA
id : cds-WP_078451435.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_254055.1
locus_tag : NS86_RS00010
name : WP_078451435.1
ontology_term : GO:0055085,GO:0016020
parent : gene-NS86_RS00010
product : ABC transporter permease subunit
protein_id : WP_078451435.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271932/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTPX01000001.1 Protein Homology CDS 1745 3778 . + 0 ID=cds-WP_078451435.1;Parent=gene-NS86_RS00010;Dbxref=GenBank:WP_078451435.1;Name=WP_078451435.1;Ontology_term=GO:0055085,GO:0016020;gbkey=CDS;go_component=membrane|0016020||IEA;go_process=transmembrane transport|0055085||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_254055.1;locus_tag=NS86_RS00010;product=ABC transporter permease subunit;protein_id=WP_078451435.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS86_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS86_RS00015' for NZ_JTPX01000001.1 Protein Homology CDS 3797 5473 +
dbxref : GenBank:WP_003096667.1
gbkey : CDS
gene : pstA
go_component : plasma membrane|0005886||IEA,ATP-binding cassette (ABC) transporter complex%2C substrate-binding subunit-containing|0055052||IEA
go_function : ATPase-coupled phosphate ion transmembrane transporter activity|0015415||IEA
go_process : phosphate ion transport|0006817||IEA
id : cds-WP_003096667.1
inference : COORDINATES: similar to |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271933/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271933/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271933/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271933/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271933/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS81_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS81_RS00005' for NZ_JTQC01000001.1 Protein Homology CDS 0 1704 -
dbxref : GenBank:WP_034011008.1
gbkey : CDS
gene : pctA
id : cds-WP_034011008.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252999.1
locus_tag : NS81_RS00005
name : WP_034011008.1
parent : gene-NS81_RS00005
partial : true
product : methyl-accepting chemotaxis protein PctA
protein_id : WP_034011008.1
source : Protein Homology
start_range : .,1
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271933/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQC01000001.1 Protein Homology CDS 1 1705 . - 0 ID=cds-WP_034011008.1;Parent=gene-NS81_RS00005;Dbxref=GenBank:WP_034011008.1;Name=WP_034011008.1;gbkey=CDS;gene=pctA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252999.1;locus_tag=NS81_RS00005;partial=true;product=methyl-accepting chemotaxis protein PctA;protein_id=WP_034011008.1;start_range=.,1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS81_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS81_RS00010' for NZ_JTQC01000001.1 Protein Homology CDS 2104 3594 +
dbxref : GenBank:WP_003114975.1
gbkey : CDS
go_function : ATP binding|0005524||IEA
id : cds-WP_003114975.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252998.1
locus_tag : NS81_RS00010
name : WP_003114975.1
ontology_term : GO:0005524
parent : gene-NS81_RS00010
product : helicase HerA-like C-terminal domain-containing protein
protein_id : WP_003114975.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271933/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQC01000001.1 Protein Homology CDS 2105 3595 . + 0 ID=cds-WP_003114975.1;Parent=gene-NS81_RS00010;Dbxref=GenBank:WP_003114975.1;Name=WP_003114975.1;Ontology_term=GO:0005524;gbkey=CDS;go_function=ATP binding|0005524||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252998.1;locus_tag=NS81_RS00010;product=helicase HerA-like C-terminal domain-containing protein;protein_id=WP_003114975.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS81_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS81_RS00015' for NZ_JTQC01000001.1 Protein Homology CDS 3698 5596 -
dbxref : GenBank:WP_004348099.1
gbkey : CDS
gene : pctC
id : cds-WP_004348099.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252997.1
locus_tag : NS81_RS00015
name : WP_004348099.1
parent : gene-NS81_RS00015
product : methyl-accepting chemotaxis protein PctC
protein_id : WP_004348099.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271933/working/snpeff_output/Pseudomonasa |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271934/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72271934/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72271934/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72271934/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72271934/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS82_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS82_RS00005' for NZ_JTQB01000001.1 Protein Homology CDS 379 450 +
dbxref : GenBank:WP_003106462.1
gbkey : CDS
gene : pqqA
go_function : catalytic activity|0003824||IEA
go_process : pyrroloquinoline quinone biosynthetic process|0018189||IEA
id : cds-WP_003106462.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250675.1
locus_tag : NS82_RS00005
name : WP_003106462.1
ontology_term : GO:0018189,GO:0003824
parent : gene-NS82_RS00005
product : pyrroloquinoline quinone precursor peptide PqqA
protein_id : WP_003106462.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271934/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_JTQB01000001.1 Protein Homology CDS 380 451 . + 0 ID=cds-WP_003106462.1;Parent=gene-NS82_RS00005;Dbxref=GenBank:WP_003106462.1;Name=WP_003106462.1;Ontology_term=GO:0018189,GO:0003824;gbkey=CDS;gene=pqqA;go_function=catalytic activity|0003824||IEA;go_process=pyrroloquinoline quinone biosynthetic process|0018189||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250675.1;locus_tag=NS82_RS00005;product=pyrroloquinoline quinone precursor peptide PqqA;protein_id=WP_003106462.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS82_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS82_RS00010' for NZ_JTQB01000001.1 Protein Homology CDS 503 1417 +
dbxref : GenBank:WP_003106464.1
gbkey : CDS
gene : pqqB
go_process : pyrroloquinoline quinone biosynthetic process|0018189||IEA
id : cds-WP_003106464.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_250676.1
locus_tag : NS82_RS00010
name : WP_003106464.1
ontology_term : GO:0018189
parent : gene-NS82_RS00010
product : pyrroloquinoline quinone biosynthesis protein PqqB
protein_id : WP_003106464.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72271934/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_JTQB01000001.1 Protein Homology CDS 504 1418 . + 0 ID=cds-WP_003106464.1;Parent=gene-NS82_RS00010;Dbxref=GenBank:WP_003106464.1;Name=WP_003106464.1;Ontology_term=GO:0018189;gbkey=CDS;gene=pqqB;go_process=pyrroloquinoline quinone biosynthetic process|0018189||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_250676.1;locus_tag=NS82_RS00010;product=pyrroloquinoline quinone biosynthesis protein PqqB;protein_id=WP_003106464.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-NS82_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-NS82_RS00015' for NZ_JTQB01000001.1 Protein Homology CDS 1427 2179 +
dbxref : GenBank:WP_003111679.1
gbkey : CDS
gene : pqqC
go_process : pyrroloquinoline quinone biosynthetic process |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/273/72273625/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/273/72273625/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' hg38'
00:00:00 Reading config file: /corral4/main/jobs/072/273/72273625/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: ' hg38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/273/72273995/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/273/72273995/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRhg38'
00:00:00 Reading config file: /corral4/main/jobs/072/273/72273995/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-5/snpEff.config
java.lang.RuntimeException: Property: 'GRhg38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:01 Logging
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/290/72290010/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/290/72290010/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRch38.86'
00:00:00 Reading config file: /corral4/main/jobs/072/290/72290010/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRch38.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/290/72290119/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/290/72290119/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRch38.86'
00:00:00 Reading config file: /corral4/main/jobs/072/290/72290119/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRch38.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72290703/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72290703/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.86, mm10 etc.'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72290703/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.86, mm10 etc..genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/290/72290741/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/290/72290741/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.36'
00:00:00 Reading config file: /corral4/main/jobs/072/290/72290741/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.36.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/299/72299742/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/299/72299742/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm39.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72304892/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72304892/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72304892/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/307/72307351/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/307/72307351/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'testHg19Chr8'
00:00:00 Reading config file: /corral4/main/jobs/072/307/72307351/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
00:00:01 done
00:00:01 Downloading database for 'testHg19Chr8'
00:00:01 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testHg19Chr8.zip' to local file '/corral4/main/jobs/072/307/72307351/tmp/snpEff_v5_2_testHg19Chr8.zip'
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testHg19Chr8.zip
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testHg19Chr8.zip, using proxy: false
00:00:03 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testHg19Chr8.zip
00:00:03 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testHg19Chr8.zip' to local file '/corral4/main/jobs/072/307/72307351/tmp/snpEff_v5_0_testHg19Chr8.zip'
00:00:03 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testHg19Chr8.zip
00:00:03 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testHg19Chr8.zip, using proxy: false
00:00:03 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testHg19Chr8.zip
00:00:03 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testHg19Chr8.zip' to local file '/corral4/main/jobs/072/307/72307351/tmp/snpEff_v5_1_testHg19Chr8.zip'
00:00:03 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testHg19Chr8.zip
00:00:03 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testHg19Chr8.zip, using proxy: false
00:00:03 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testHg19Chr8.zip
FATAL ERROR: Failed to download database from [https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testHg19Chr8.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testHg19Chr8.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testHg19Chr8.zip] |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72307402/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72307402/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo_sapiens(UCSC)'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72307402/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo_sapiens(UCSC).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/312/72312692/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/312/72312692/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/312/72312692/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-5/snpEff.config
00:00:01 done
00:00:01 Downloading database for 'hg19'
00:00:02 Connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_hg19.zip
00:00:04 Local file name: '/corral4/main/jobs/072/312/72312692/tmp/snpEff_v4_3_hg19.zip'
.............................................................................................................................................................................................................................................................................................
00:05:16 Donwload finished. Total 311872883 bytes.
00:05:16 Extracting file 'data/hg19/interactions.bin'
00:05:16 Creating local directory: '/corral4/main/jobs/072/312/72312692/outputs/dataset_0329f0a1-e88f-4d17-ac3f-ec42cc4101f8_files/hg19'
00:05:16 Extracting file 'data/hg19/nextProt.bin'
00:05:16 Extracting file 'data/hg19/pwms.bin'
00:05:16 Extracting file 'data/hg19/sequence.10.bin'
00:05:17 Extracting file 'data/hg19/sequence.11.bin'
00:05:17 Extracting file 'data/hg19/sequence.12.bin'
00:05:17 Extracting file 'data/hg19/sequence.13.bin'
00:05:17 Extracting file 'data/hg19/sequence.14.bin'
00:05:17 Extracting file 'data/hg19/sequence.15.bin'
00:05:17 Extracting file 'data/hg19/sequence.16.bin'
00:05:18 Extracting file 'data/hg19/sequence.17.bin'
00:05:18 Extracting file 'data/hg19/sequence.17_ctg5_hap1.bin'
00:05:18 Extracting file 'data/hg19/sequence.18.bin'
00:05:18 Extracting file 'data/hg19/sequence.19.bin'
00:05:18 Extracting file 'data/hg19/sequence.1.bin'
00:05:18 Extracting file 'data/hg19/sequence.20.bin'
00:05:18 Extracting file 'data/hg19/sequence.21.bin'
00:05:18 Extracting file 'data/hg19/sequence.22.bin'
00:05:18 Extracting file 'data/hg19/sequence.2.bin'
00:05:19 Extracting file 'data/hg19/sequence.3.bin'
00:05:19 Extracting file 'data/hg19/sequence.4.bin'
00:05:19 Extracting file 'data/hg19/sequence.5.bin'
00:05:19 Extracting file 'data/hg19/sequence.6_apd_hap1.bin'
00:05:19 Extracting file 'data/hg19/sequence.6.bin'
java.lang.RuntimeException: java.io.EOFException: Unexpected end of ZLIB input stream
at org.snpeff.util.Download.unzip(Download.java:296)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:33)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:86)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
Caused by: java.io.EOFException: Unexpected end of ZLIB input stream
at java.base/java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:245)
at java.base/java.util.zip.InflaterInputStream.read(InflaterInputStream.java:159)
at java.base/java.util.zip.ZipInputStream.read(ZipInputStream.java:195)
at org.snpeff.util.Download.unzip(Download.java:275)
... 5 more
00:05:19 Logging
00:05:20 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/312/72312968/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/312/72312968/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/312/72312968/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/313/72313366/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/313/72313366/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg38'
00:00:00 Reading config file: /corral4/main/jobs/072/313/72313366/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-5/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:01 Logging
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/314/72314240/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/314/72314240/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Human Dec.2013 (GRCh38/hg38)(hg38)'
00:00:00 Reading config file: /corral4/main/jobs/072/314/72314240/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Human Dec.2013 (GRCh38/hg38)(hg38).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/314/72314241/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/314/72314241/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Human Dec. 2013 (GRCh38/hg38)(hg38)'
00:00:00 Reading config file: /corral4/main/jobs/072/314/72314241/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Human Dec. 2013 (GRCh38/hg38)(hg38).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72314909/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72314909/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'EF'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'EF'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72314909/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'EF'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72314909/working/snpeff_output/EF/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72314909/working/snpeff_output/EF/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00005' for CP038996.1 Protein Homology CDS 0 1334 +
dbxref : NCBI_GP:QHU86234.1
gbkey : CDS
gene : dnaA
id : cds-QHU86234.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_813814.1
locus_tag : E6A31_00005
name : QHU86234.1
parent : gene-E6A31_00005
product : chromosomal replication initiator protein DnaA
protein_id : QHU86234.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72314909/working/snpeff_output/EF/genes.gff' line 12 'CP038996.1 Protein Homology CDS 1 1335 . + 0 ID=cds-QHU86234.1;Parent=gene-E6A31_00005;Dbxref=NCBI_GP:QHU86234.1;Name=QHU86234.1;gbkey=CDS;gene=dnaA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_813814.1;locus_tag=E6A31_00005;product=chromosomal replication initiator protein DnaA;protein_id=QHU86234.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00010' for CP038996.1 Protein Homology CDS 1532 2662 +
dbxref : NCBI_GP:QHU86235.1
gbkey : CDS
gene : dnaN
id : cds-QHU86235.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1
locus_tag : E6A31_00010
name : QHU86235.1
parent : gene-E6A31_00010
product : DNA polymerase III subunit beta
protein_id : QHU86235.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72314909/working/snpeff_output/EF/genes.gff' line 14 'CP038996.1 Protein Homology CDS 1533 2663 . + 0 ID=cds-QHU86235.1;Parent=gene-E6A31_00010;Dbxref=NCBI_GP:QHU86235.1;Name=QHU86235.1;gbkey=CDS;gene=dnaN;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1;locus_tag=E6A31_00010;product=DNA polymerase III subunit beta;protein_id=QHU86235.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00015' for CP038996.1 Protein Homology CDS 2891 3133 +
dbxref : NCBI_GP:QHU86236.1
gbkey : CDS
gene : yaaA
id : cds-QHU86236.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1
locus_tag : E6A31_00015
name : QHU86236.1
parent : gene-E6A31_00015
product : S4 domain-containing protein YaaA
protein_id : QHU86236.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72314909/working/snpeff_output/EF/genes.gff' line 16 'CP038996.1 Protein Homology CDS 2892 3134 . + 0 ID=cds-QHU86236.1;Parent=gene-E6A31_00015;Dbxref=NCBI_GP:QHU86236.1;Name=QHU86236.1;gbkey=CDS;gene=yaaA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1;locus_tag=E6A31_00015;product=S4 domain-containing protein YaaA;protein_id=QHU86236.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00020' is a Gene instead of a transcript. Created transcript ' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72314970/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72314970/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'EF_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'EF_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72314970/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'EF_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72314970/working/snpeff_output/EF_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72314970/working/snpeff_output/EF_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00005' for CP038996.1 Protein Homology CDS 0 1334 +
dbxref : NCBI_GP:QHU86234.1
gbkey : CDS
gene : dnaA
id : cds-QHU86234.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_813814.1
locus_tag : E6A31_00005
name : QHU86234.1
parent : gene-E6A31_00005
product : chromosomal replication initiator protein DnaA
protein_id : QHU86234.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72314970/working/snpeff_output/EF_gff/genes.gff' line 12 'CP038996.1 Protein Homology CDS 1 1335 . + 0 ID=cds-QHU86234.1;Parent=gene-E6A31_00005;Dbxref=NCBI_GP:QHU86234.1;Name=QHU86234.1;gbkey=CDS;gene=dnaA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_813814.1;locus_tag=E6A31_00005;product=chromosomal replication initiator protein DnaA;protein_id=QHU86234.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00010' for CP038996.1 Protein Homology CDS 1532 2662 +
dbxref : NCBI_GP:QHU86235.1
gbkey : CDS
gene : dnaN
id : cds-QHU86235.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1
locus_tag : E6A31_00010
name : QHU86235.1
parent : gene-E6A31_00010
product : DNA polymerase III subunit beta
protein_id : QHU86235.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72314970/working/snpeff_output/EF_gff/genes.gff' line 14 'CP038996.1 Protein Homology CDS 1533 2663 . + 0 ID=cds-QHU86235.1;Parent=gene-E6A31_00010;Dbxref=NCBI_GP:QHU86235.1;Name=QHU86235.1;gbkey=CDS;gene=dnaN;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1;locus_tag=E6A31_00010;product=DNA polymerase III subunit beta;protein_id=QHU86235.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00015' for CP038996.1 Protein Homology CDS 2891 3133 +
dbxref : NCBI_GP:QHU86236.1
gbkey : CDS
gene : yaaA
id : cds-QHU86236.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1
locus_tag : E6A31_00015
name : QHU86236.1
parent : gene-E6A31_00015
product : S4 domain-containing protein YaaA
protein_id : QHU86236.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72314970/working/snpeff_output/EF_gff/genes.gff' line 16 'CP038996.1 Protein Homology CDS 2892 3134 . + 0 ID=cds-QHU86236.1;Parent=gene-E6A31_00015;Dbxref=NCBI_GP:QHU86236.1;Name=QHU86236.1;gbkey=CDS;gene=yaaA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1;locus_tag=E6A31_00015;product=S4 domain-containing protein YaaA;protein_id=QHU86236.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00020' is a Gene instead of a tra |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72315012/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72315012/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'EF_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'EF_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72315012/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'EF_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72315012/working/snpeff_output/EF_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72315012/working/snpeff_output/EF_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00005' for CP038996.1 Protein Homology CDS 0 1334 +
dbxref : NCBI_GP:QHU86234.1
gbkey : CDS
gene : dnaA
id : cds-QHU86234.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_813814.1
locus_tag : E6A31_00005
name : QHU86234.1
parent : gene-E6A31_00005
product : chromosomal replication initiator protein DnaA
protein_id : QHU86234.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72315012/working/snpeff_output/EF_gff/genes.gff' line 12 'CP038996.1 Protein Homology CDS 1 1335 . + 0 ID=cds-QHU86234.1;Parent=gene-E6A31_00005;Dbxref=NCBI_GP:QHU86234.1;Name=QHU86234.1;gbkey=CDS;gene=dnaA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_813814.1;locus_tag=E6A31_00005;product=chromosomal replication initiator protein DnaA;protein_id=QHU86234.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00010' for CP038996.1 Protein Homology CDS 1532 2662 +
dbxref : NCBI_GP:QHU86235.1
gbkey : CDS
gene : dnaN
id : cds-QHU86235.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1
locus_tag : E6A31_00010
name : QHU86235.1
parent : gene-E6A31_00010
product : DNA polymerase III subunit beta
protein_id : QHU86235.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72315012/working/snpeff_output/EF_gff/genes.gff' line 14 'CP038996.1 Protein Homology CDS 1533 2663 . + 0 ID=cds-QHU86235.1;Parent=gene-E6A31_00010;Dbxref=NCBI_GP:QHU86235.1;Name=QHU86235.1;gbkey=CDS;gene=dnaN;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1;locus_tag=E6A31_00010;product=DNA polymerase III subunit beta;protein_id=QHU86235.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00015' for CP038996.1 Protein Homology CDS 2891 3133 +
dbxref : NCBI_GP:QHU86236.1
gbkey : CDS
gene : yaaA
id : cds-QHU86236.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1
locus_tag : E6A31_00015
name : QHU86236.1
parent : gene-E6A31_00015
product : S4 domain-containing protein YaaA
protein_id : QHU86236.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72315012/working/snpeff_output/EF_gff/genes.gff' line 16 'CP038996.1 Protein Homology CDS 2892 3134 . + 0 ID=cds-QHU86236.1;Parent=gene-E6A31_00015;Dbxref=NCBI_GP:QHU86236.1;Name=QHU86236.1;gbkey=CDS;gene=yaaA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1;locus_tag=E6A31_00015;product=S4 domain-containing protein YaaA;protein_id=QHU86236.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00020' is a Gene instead of a tra |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/315/72315114/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/315/72315114/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.36'
00:00:00 Reading config file: /corral4/main/jobs/072/315/72315114/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.36.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316291/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316291/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'AB_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'AB_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72316291/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'AB_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72316291/working/snpeff_output/AB_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72316291/working/snpeff_output/AB_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316291/working/snpeff_output/AB_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316291/working/snpeff_output/AB_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316291/working/snpeff_output/AB_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316472/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316472/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SA_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SA_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72316472/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SA_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72316472/working/snpeff_output/SA_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72316472/working/snpeff_output/SA_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316472/working/snpeff_output/SA_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316472/working/snpeff_output/SA_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316472/working/snpeff_output/SA_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316560/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316560/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72316560/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72316560/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72316560/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316560/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316560/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316560/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316588/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72316588/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Se_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Se_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72316588/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Se_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72316588/working/snpeff_output/Se_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72316588/working/snpeff_output/Se_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for NC_003197.2 RefSeq CDS 189 254 +
dbxref : GenBank:NP_459006.1,GeneID:1251519
gbkey : CDS
gene : thrL
id : cds-NP_459006.1
locus_tag : STM0001
name : NP_459006.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : NP_459006.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316588/working/snpeff_output/Se_gff/genes.gff' line 10 'NC_003197.2 RefSeq CDS 190 255 . + 0 ID=cds-NP_459006.1;Parent=gene-STM0001;Dbxref=GenBank:NP_459006.1,GeneID:1251519;Name=NP_459006.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=NP_459006.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for NC_003197.2 RefSeq CDS 336 2798 +
dbxref : GenBank:NP_459007.1,GeneID:1251520
gbkey : CDS
gene : thrA
id : cds-NP_459007.1
locus_tag : STM0002
name : NP_459007.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : NP_459007.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72316588/working/snpeff_output/Se_gff/genes.gff' line 12 'NC_003197.2 RefSeq CDS 337 2799 . + 0 ID=cds-NP_459007.1;Parent=gene-STM0002;Dbxref=GenBank:NP_459007.1,GeneID:1251520;Name=NP_459007.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=NP_459007.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for NC_003197.2 RefSeq CDS 2800 3729 +
dbxref : GenBank:NP_459008.1,GeneID:1251521
gbkey : CDS
gene : thrB
id : cds-NP_459008.1
locus_tag : STM0003
name : NP_459008.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : NP_459008.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstrea |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317008/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317008/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'ASM694v2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'ASM694v2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72317008/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'ASM694v2'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72317008/working/snpeff_output/ASM694v2/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72317008/working/snpeff_output/ASM694v2/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317008/working/snpeff_output/ASM694v2/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317008/working/snpeff_output/ASM694v2/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317008/working/snpeff_output/ASM694v2/genes.gff' line |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317347/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317347/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'GCA_000006945.2_ASM694v2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCA_000006945.2_ASM694v2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72317347/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'GCA_000006945.2_ASM694v2'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72317347/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72317347/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317347/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317347/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317359/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317359/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'EF_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'EF_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72317359/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'EF_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72317359/working/snpeff_output/EF_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72317359/working/snpeff_output/EF_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00005' for CP038996.1 Protein Homology CDS 0 1334 +
dbxref : NCBI_GP:QHU86234.1
gbkey : CDS
gene : dnaA
id : cds-QHU86234.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_813814.1
locus_tag : E6A31_00005
name : QHU86234.1
parent : gene-E6A31_00005
product : chromosomal replication initiator protein DnaA
protein_id : QHU86234.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317359/working/snpeff_output/EF_gff/genes.gff' line 12 'CP038996.1 Protein Homology CDS 1 1335 . + 0 ID=cds-QHU86234.1;Parent=gene-E6A31_00005;Dbxref=NCBI_GP:QHU86234.1;Name=QHU86234.1;gbkey=CDS;gene=dnaA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_813814.1;locus_tag=E6A31_00005;product=chromosomal replication initiator protein DnaA;protein_id=QHU86234.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00010' for CP038996.1 Protein Homology CDS 1532 2662 +
dbxref : NCBI_GP:QHU86235.1
gbkey : CDS
gene : dnaN
id : cds-QHU86235.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1
locus_tag : E6A31_00010
name : QHU86235.1
parent : gene-E6A31_00010
product : DNA polymerase III subunit beta
protein_id : QHU86235.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317359/working/snpeff_output/EF_gff/genes.gff' line 14 'CP038996.1 Protein Homology CDS 1533 2663 . + 0 ID=cds-QHU86235.1;Parent=gene-E6A31_00010;Dbxref=NCBI_GP:QHU86235.1;Name=QHU86235.1;gbkey=CDS;gene=dnaN;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002288361.1;locus_tag=E6A31_00010;product=DNA polymerase III subunit beta;protein_id=QHU86235.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-E6A31_00015' for CP038996.1 Protein Homology CDS 2891 3133 +
dbxref : NCBI_GP:QHU86236.1
gbkey : CDS
gene : yaaA
id : cds-QHU86236.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1
locus_tag : E6A31_00015
name : QHU86236.1
parent : gene-E6A31_00015
product : S4 domain-containing protein YaaA
protein_id : QHU86236.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317359/working/snpeff_output/EF_gff/genes.gff' line 16 'CP038996.1 Protein Homology CDS 2892 3134 . + 0 ID=cds-QHU86236.1;Parent=gene-E6A31_00015;Dbxref=NCBI_GP:QHU86236.1;Name=QHU86236.1;gbkey=CDS;gene=yaaA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002293125.1;locus_tag=E6A31_00015;product=S4 domain-containing protein YaaA;protein_id=QHU86236.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-E6A31_00020' is a Gene instead of a tra |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317475/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317475/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'GCA_000006945.2_ASM694v2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCA_000006945.2_ASM694v2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72317475/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'GCA_000006945.2_ASM694v2'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72317475/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72317475/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317475/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72317475/working/snpeff_output/GCA_000006945.2_ASM694v2/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317556/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317556/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317557/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317557/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317558/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317558/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317559/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317559/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317560/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317560/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317561/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317561/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317562/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317562/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317563/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317563/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317564/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317564/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317565/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317565/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317566/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317566/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317567/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317567/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317568/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317568/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317569/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317569/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317570/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317570/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317571/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317571/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317572/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317572/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317573/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317573/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317574/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317574/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317575/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317575/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317576/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317576/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317577/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317577/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317578/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317578/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317579/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317579/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317580/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317580/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317581/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317581/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317582/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317582/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317583/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317583/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317584/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317584/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317585/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317585/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317586/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317586/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317587/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317587/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317588/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317588/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317589/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317589/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317590/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317590/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317591/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317591/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317592/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317592/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317593/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317593/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317594/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317594/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317595/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317595/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317596/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317596/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317597/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317597/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317598/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317598/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317599/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317599/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317600/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317600/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317601/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317601/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317602/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317602/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317603/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317603/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317604/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317604/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317605/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317605/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317606/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317606/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317607/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317607/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317608/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317608/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317609/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317609/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317610/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317610/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317611/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317611/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317612/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317612/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317613/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317613/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317614/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317614/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317615/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317615/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317616/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317616/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317617/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317617/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317618/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317618/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317619/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317619/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317620/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317620/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317621/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317621/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317622/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317622/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317623/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317623/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317624/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317624/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317625/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317625/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317626/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317626/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317627/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317627/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317628/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317628/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317629/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317629/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317630/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317630/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317631/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317631/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317632/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317632/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317633/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317633/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317634/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317634/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317635/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317635/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317636/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317636/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317637/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317637/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317638/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317638/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317639/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317639/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317640/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317640/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317641/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317641/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317642/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317642/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317643/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317643/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317644/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317644/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317645/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317645/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317646/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317646/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317647/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317647/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317648/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317648/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317649/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317649/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317650/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317650/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317651/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317651/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317652/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317652/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317653/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317653/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317654/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317654/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317655/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317655/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317656/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317656/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317657/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317657/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317658/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317658/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317659/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317659/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317660/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317660/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317661/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317661/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317662/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317662/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317663/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317663/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317664/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317664/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317665/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317665/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317666/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317666/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317667/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317667/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317668/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317668/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317669/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317669/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317670/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317670/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317671/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317671/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317672/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317672/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317673/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317673/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317674/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317674/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317675/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317675/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317676/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317676/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317677/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317677/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317678/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317678/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317679/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317679/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317680/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317680/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317681/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317681/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317682/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317682/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317683/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317683/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317684/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317684/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317685/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317685/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317686/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317686/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317687/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317687/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317688/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317688/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317689/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317689/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317690/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317690/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317691/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317691/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317692/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317692/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317693/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317693/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317694/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317694/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317695/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317695/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317696/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317696/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317697/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317697/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317698/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317698/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317699/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317699/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317700/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317700/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317701/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317701/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317702/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317702/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317703/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317703/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317704/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317704/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317705/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317705/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317706/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317706/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317707/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317707/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317708/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317708/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317709/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317709/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317710/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72317710/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317711/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317711/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317712/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317712/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317713/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317713/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317714/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317714/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317715/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317715/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317716/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317716/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317717/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317717/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317718/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317718/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317719/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317719/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317720/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317720/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317721/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317721/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317722/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317722/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317723/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317723/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317724/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317724/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317725/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317725/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317726/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317726/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317727/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317727/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317728/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317728/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317729/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317729/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317730/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317730/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317731/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317731/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317732/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317732/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317733/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/317/72317733/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'EF.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/320/72320196/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/320/72320196/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/320/72320507/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/320/72320507/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'homo sapiens : hg38'
00:00:00 Reading config file: /corral4/main/jobs/072/320/72320507/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'homo sapiens : hg38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/320/72320581/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/320/72320581/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg38'
00:00:00 Reading config file: /corral4/main/jobs/072/320/72320581/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72325999/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72325999/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'hg38.fa.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72327942/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72327942/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72327942/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72327942/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72327942/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72327942/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72327942/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72327942/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72327981/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72327981/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SA'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SA'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72327981/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SA'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72327981/working/snpeff_output/SA/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72327981/working/snpeff_output/SA/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72327981/working/snpeff_output/SA/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72327981/working/snpeff_output/SA/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72327981/working/snpeff_output/SA/genes.gff' line 15 'AE006468.2 Genbank CDS 2801 3730 . + 0 ID=c |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328035/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328035/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72328035/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72328035/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72328035/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328035/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328035/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328035/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328076/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328076/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72328076/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72328076/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72328076/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for NC_003197.2 RefSeq CDS 189 254 +
dbxref : GenBank:NP_459006.1,GeneID:1251519
gbkey : CDS
gene : thrL
id : cds-NP_459006.1
locus_tag : STM0001
name : NP_459006.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : NP_459006.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328076/working/snpeff_output/SE_gff/genes.gff' line 10 'NC_003197.2 RefSeq CDS 190 255 . + 0 ID=cds-NP_459006.1;Parent=gene-STM0001;Dbxref=GenBank:NP_459006.1,GeneID:1251519;Name=NP_459006.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=NP_459006.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for NC_003197.2 RefSeq CDS 336 2798 +
dbxref : GenBank:NP_459007.1,GeneID:1251520
gbkey : CDS
gene : thrA
id : cds-NP_459007.1
locus_tag : STM0002
name : NP_459007.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : NP_459007.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328076/working/snpeff_output/SE_gff/genes.gff' line 12 'NC_003197.2 RefSeq CDS 337 2799 . + 0 ID=cds-NP_459007.1;Parent=gene-STM0002;Dbxref=GenBank:NP_459007.1,GeneID:1251520;Name=NP_459007.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=NP_459007.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for NC_003197.2 RefSeq CDS 2800 3729 +
dbxref : GenBank:NP_459008.1,GeneID:1251521
gbkey : CDS
gene : thrB
id : cds-NP_459008.1
locus_tag : STM0003
name : NP_459008.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : NP_459008.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstrea |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328197/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328197/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72328197/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72328197/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72328197/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328197/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328197/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328197/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328793/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72328793/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72328793/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72328793/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72328793/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328793/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328793/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72328793/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329696/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329696/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329697/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329697/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329698/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329698/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329699/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329699/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329700/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329700/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329701/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329701/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329702/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329702/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329703/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329703/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329704/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329704/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329706/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329706/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329710/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329710/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329711/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329711/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329712/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329712/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329713/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329713/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329714/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329714/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329715/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329715/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329716/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329716/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329717/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329717/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329718/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329718/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329719/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329719/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329728/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329728/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329729/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329729/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329730/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329730/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329731/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329731/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329732/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329732/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329733/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329733/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329734/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329734/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329735/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329735/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329744/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329744/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329745/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329745/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329746/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329746/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329747/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329747/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329748/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329748/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329749/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329749/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329750/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329750/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329751/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329751/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329752/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329752/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329753/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329753/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329792/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329792/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329793/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329793/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329794/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329794/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329795/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329795/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329808/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72329808/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329825/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329825/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329827/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329827/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329829/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329829/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329830/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329830/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329831/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329831/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329832/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329832/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329833/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329833/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329836/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329836/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329837/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329837/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329838/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329838/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329839/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329839/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329840/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329840/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329841/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329841/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329842/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329842/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329843/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329843/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329844/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329844/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329846/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329846/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329847/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329847/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329849/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329849/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329850/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329850/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329851/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329851/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329854/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329854/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329856/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329856/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329857/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329857/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329860/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329860/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329862/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329862/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329865/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329865/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329866/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329866/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329867/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329867/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329868/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329868/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329869/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329869/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329870/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329870/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329872/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329872/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329873/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329873/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329874/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329874/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329875/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329875/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329877/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329877/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329878/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329878/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329883/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329883/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329885/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329885/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329886/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329886/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329887/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329887/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329888/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329888/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329889/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329889/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329890/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329890/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329891/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329891/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329892/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329892/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329893/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329893/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329894/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329894/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329895/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/329/72329895/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S_pneumoniae_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/331/72331168/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/331/72331168/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Spn_TIGR4.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/333/72333779/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/333/72333779/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg 19'
00:00:00 Reading config file: /corral4/main/jobs/072/333/72333779/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'hg 19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/333/72333796/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/333/72333796/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg19_chr8'
00:00:00 Reading config file: /corral4/main/jobs/072/333/72333796/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'hg19_chr8.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334248/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334248/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334249/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334249/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334250/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334250/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334251/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334251/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334252/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334252/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334253/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334253/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334254/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334254/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334255/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334255/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334256/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334256/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334257/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334257/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334258/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334258/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334259/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334259/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334260/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334260/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334261/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334261/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334262/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334262/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334263/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334263/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334264/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334264/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334265/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334265/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334266/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334266/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334267/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334267/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334268/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334268/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334269/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334269/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334270/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334270/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334271/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334271/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334272/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334272/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334273/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334273/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334274/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334274/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334275/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334275/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334276/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334276/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334277/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334277/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334278/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334278/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334279/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334279/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334280/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334280/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334281/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334281/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334282/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334282/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334283/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334283/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334284/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334284/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334285/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334285/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334286/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334286/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334287/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334287/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334288/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334288/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334289/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334289/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334290/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334290/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334291/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334291/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334292/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334292/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334293/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334293/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334294/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334294/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334295/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334295/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334296/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334296/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334297/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334297/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334298/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334298/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334299/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334299/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334300/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334300/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334301/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334301/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334302/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334302/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334303/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334303/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334304/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334304/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334305/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334305/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334306/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334306/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334307/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334307/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334308/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334308/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334309/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334309/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334310/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334310/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334311/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334311/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334312/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334312/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334313/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334313/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334314/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334314/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334315/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334315/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334316/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334316/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334317/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334317/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334318/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334318/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334319/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334319/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334320/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334320/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334321/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334321/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334322/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334322/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334323/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334323/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334324/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334324/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334325/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334325/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334326/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334326/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334327/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334327/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334328/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334328/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334329/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334329/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334330/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334330/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334331/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334331/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334332/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334332/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334333/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334333/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334334/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334334/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334335/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334335/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334336/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334336/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334337/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334337/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334338/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334338/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334339/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334339/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334340/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334340/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334341/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334341/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334342/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334342/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334343/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334343/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334344/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334344/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334345/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334345/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334346/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334346/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334347/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334347/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334348/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334348/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334349/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334349/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334350/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334350/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334351/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334351/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334352/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334352/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334353/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334353/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334354/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334354/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334355/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334355/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334356/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334356/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334357/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334357/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334358/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334358/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334359/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334359/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334360/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334360/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334361/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334361/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334362/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334362/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334363/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334363/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334364/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334364/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334365/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334365/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334366/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334366/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334367/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334367/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334368/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334368/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334369/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334369/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334370/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334370/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334371/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334371/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334372/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334372/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334373/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334373/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334374/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334374/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334376/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334376/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334377/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334377/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334378/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334378/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334379/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334379/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334380/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334380/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334381/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334381/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334382/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334382/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334383/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334383/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334384/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334384/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334385/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334385/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334386/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334386/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334387/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334387/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334388/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334388/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334389/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334389/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334390/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334390/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334391/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334391/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334392/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334392/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334393/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334393/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334394/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334394/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334395/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334395/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334396/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334396/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334397/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334397/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334398/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334398/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334399/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334399/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334400/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334400/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334401/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334401/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334402/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334402/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334403/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334403/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334404/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334404/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334405/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334405/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334407/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334407/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334408/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334408/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334409/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334409/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334410/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334410/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334411/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334411/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334412/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334412/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334413/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334413/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334414/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334414/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334415/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334415/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334416/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334416/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334417/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334417/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334418/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334418/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334419/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334419/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334420/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334420/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334421/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334421/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334422/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72334422/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334424/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334424/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334426/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334426/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334427/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/334/72334427/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobac.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72336203/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72336203/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72336203/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72336203/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72336203/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336203/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336203/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336203/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72336422/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72336422/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72336422/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72336422/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72336422/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for NC_003197.2 RefSeq CDS 189 254 +
dbxref : GenBank:NP_459006.1,GeneID:1251519
gbkey : CDS
gene : thrL
id : cds-NP_459006.1
locus_tag : STM0001
name : NP_459006.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : NP_459006.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336422/working/snpeff_output/SE_gff/genes.gff' line 10 'NC_003197.2 RefSeq CDS 190 255 . + 0 ID=cds-NP_459006.1;Parent=gene-STM0001;Dbxref=GenBank:NP_459006.1,GeneID:1251519;Name=NP_459006.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=NP_459006.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for NC_003197.2 RefSeq CDS 336 2798 +
dbxref : GenBank:NP_459007.1,GeneID:1251520
gbkey : CDS
gene : thrA
id : cds-NP_459007.1
locus_tag : STM0002
name : NP_459007.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : NP_459007.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336422/working/snpeff_output/SE_gff/genes.gff' line 12 'NC_003197.2 RefSeq CDS 337 2799 . + 0 ID=cds-NP_459007.1;Parent=gene-STM0002;Dbxref=GenBank:NP_459007.1,GeneID:1251520;Name=NP_459007.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=NP_459007.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for NC_003197.2 RefSeq CDS 2800 3729 +
dbxref : GenBank:NP_459008.1,GeneID:1251521
gbkey : CDS
gene : thrB
id : cds-NP_459008.1
locus_tag : STM0003
name : NP_459008.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : NP_459008.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstrea |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72336552/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72336552/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72336552/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72336552/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72336552/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336552/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336552/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72336552/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72343348/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72343348/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72343348/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72343348/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72343348/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72343348/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72343348/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72343348/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72343515/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72343515/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SE_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SE_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72343515/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SE_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72343515/working/snpeff_output/SE_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72343515/working/snpeff_output/SE_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72343515/working/snpeff_output/SE_gff/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72343515/working/snpeff_output/SE_gff/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72343515/working/snpeff_output/SE_gff/genes.gff' line 15 'AE006468.2 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344418/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344418/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Neisseria_gonorrhoeae'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Neisseria_gonorrhoeae'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72344418/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Neisseria_gonorrhoeae'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72344418/working/snpeff_output/Neisseria_gonorrhoeae/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72344418/working/snpeff_output/Neisseria_gonorrhoeae/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00005' for NZ_AP023069.1 Protein Homology CDS 0 1556 +
dbxref : GenBank:WP_003687194.1,GeneID:66752266
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003687194.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1
locus_tag : HT085_RS00005
name : WP_003687194.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-HT085_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003687194.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344418/working/snpeff_output/Neisseria_gonorrhoeae/genes.gff' line 12 'NZ_AP023069.1 Protein Homology CDS 1 1557 . + 0 ID=cds-WP_003687194.1;Parent=gene-HT085_RS00005;Dbxref=GenBank:WP_003687194.1,GeneID:66752266;Name=WP_003687194.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1;locus_tag=HT085_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003687194.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00010' for NZ_AP023069.1 Protein Homology CDS 1636 2739 +
dbxref : GenBank:WP_003687195.1,GeneID:66752267
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_003687195.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009174415.1
locus_tag : HT085_RS00010
name : WP_003687195.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-HT085_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_003687195.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344418/working/snpeff_output/Neisseria_gonorrhoeae/genes.gff' line 14 'NZ_AP023069.1 Protein Homology CDS 1637 2740 . + 0 ID=cds-WP_003687195.1;Parent=gene-HT085_RS00010;Dbxref=GenBank:WP_003687195.1,GeneID:66752267;Name=WP_003687195.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activit |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344420/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344420/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Streptococcus_pneumoniae_radha'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Streptococcus_pneumoniae_radha'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72344420/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Streptococcus_pneumoniae_radha'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72344420/working/snpeff_output/Streptococcus_pneumoniae_radha/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72344420/working/snpeff_output/Streptococcus_pneumoniae_radha/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13125' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13125' for NZ_LN831051.1 Protein Homology CDS 1424 1558 +
dbxref : GenBank:WP_261291558.1,GeneID:93875613
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291558.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13125
name : WP_261291558.1
ontology_term : GO:0006096,GO:0004618
parent : gene-AT689_RS13125
product : phosphoglycerate kinase
protein_id : WP_261291558.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344420/working/snpeff_output/Streptococcus_pneumoniae_radha/genes.gff' line 14 'NZ_LN831051.1 Protein Homology CDS 1425 1559 . + 0 ID=cds-WP_261291558.1;Parent=gene-AT689_RS13125;Dbxref=GenBank:WP_261291558.1,GeneID:93875613;Name=WP_261291558.1;Ontology_term=GO:0006096,GO:0004618;gbkey=CDS;gene=pgk;go_function=phosphoglycerate kinase activity|0004618||IEA;go_process=glycolytic process|0006096||IEA;inference=COORDINATES: protein motif:HMM:NF012389.5;locus_tag=AT689_RS13125;product=phosphoglycerate kinase;protein_id=WP_261291558.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13130' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13130' for NZ_LN831051.1 Protein Homology CDS 1587 2075 +
dbxref : GenBank:WP_261291561.1,GeneID:93875614
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291561.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13130
name : WP_261291561.1
ontology_term : GO:0006096,GO:0004618
parent : gene-AT689_RS13130
product : phosphoglycerate kinase
protein_id : WP_261291561.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344420/working/snpeff_output/Streptococcus_pneumoniae_radha/genes.gff' line 16 'NZ_LN831051.1 Protein Homology CDS 1588 2076 . + 0 ID=cds-WP_261291561.1;Parent=gene-AT689_RS13130;Dbxref=GenBank:WP_261291561.1,GeneID:93875614;Name=WP_261291561.1;Ontology_term=GO:0006096,GO:0004618;gbkey=CDS;gene=pgk;go_function=phosphoglycerate kinase activity|0004618||IEA;go_process=glycolytic process|0006096||IEA;inference=COORDINATES: protein motif:HMM:NF012389.5;locus_tag=AT689_RS13130;product=phosphoglycerate kinase;protein_id=WP_261291561.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13135' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13135' for NZ_LN831051.1 Protein Homology CDS 1990 2301 +
dbxref : GenBank:WP_261291559.1,GeneID:93875615
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kina |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344490/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344490/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Spr'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Spr'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72344490/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Spr'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72344490/working/snpeff_output/Spr/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72344490/working/snpeff_output/Spr/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13125' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13125' for NZ_LN831051.1 Protein Homology CDS 1424 1558 +
dbxref : GenBank:WP_261291558.1,GeneID:93875613
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291558.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13125
name : WP_261291558.1
ontology_term : GO:0006096,GO:0004618
parent : gene-AT689_RS13125
product : phosphoglycerate kinase
protein_id : WP_261291558.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344490/working/snpeff_output/Spr/genes.gff' line 14 'NZ_LN831051.1 Protein Homology CDS 1425 1559 . + 0 ID=cds-WP_261291558.1;Parent=gene-AT689_RS13125;Dbxref=GenBank:WP_261291558.1,GeneID:93875613;Name=WP_261291558.1;Ontology_term=GO:0006096,GO:0004618;gbkey=CDS;gene=pgk;go_function=phosphoglycerate kinase activity|0004618||IEA;go_process=glycolytic process|0006096||IEA;inference=COORDINATES: protein motif:HMM:NF012389.5;locus_tag=AT689_RS13125;product=phosphoglycerate kinase;protein_id=WP_261291558.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13130' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13130' for NZ_LN831051.1 Protein Homology CDS 1587 2075 +
dbxref : GenBank:WP_261291561.1,GeneID:93875614
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291561.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13130
name : WP_261291561.1
ontology_term : GO:0006096,GO:0004618
parent : gene-AT689_RS13130
product : phosphoglycerate kinase
protein_id : WP_261291561.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344490/working/snpeff_output/Spr/genes.gff' line 16 'NZ_LN831051.1 Protein Homology CDS 1588 2076 . + 0 ID=cds-WP_261291561.1;Parent=gene-AT689_RS13130;Dbxref=GenBank:WP_261291561.1,GeneID:93875614;Name=WP_261291561.1;Ontology_term=GO:0006096,GO:0004618;gbkey=CDS;gene=pgk;go_function=phosphoglycerate kinase activity|0004618||IEA;go_process=glycolytic process|0006096||IEA;inference=COORDINATES: protein motif:HMM:NF012389.5;locus_tag=AT689_RS13130;product=phosphoglycerate kinase;protein_id=WP_261291561.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13135' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13135' for NZ_LN831051.1 Protein Homology CDS 1990 2301 +
dbxref : GenBank:WP_261291559.1,GeneID:93875615
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291559.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13135 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344494/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344494/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'NGGayathri'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NGGayathri'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72344494/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'NGGayathri'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72344494/working/snpeff_output/NGGayathri/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72344494/working/snpeff_output/NGGayathri/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00005' for NZ_AP023069.1 Protein Homology CDS 0 1556 +
dbxref : GenBank:WP_003687194.1,GeneID:66752266
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003687194.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1
locus_tag : HT085_RS00005
name : WP_003687194.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-HT085_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003687194.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344494/working/snpeff_output/NGGayathri/genes.gff' line 12 'NZ_AP023069.1 Protein Homology CDS 1 1557 . + 0 ID=cds-WP_003687194.1;Parent=gene-HT085_RS00005;Dbxref=GenBank:WP_003687194.1,GeneID:66752266;Name=WP_003687194.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1;locus_tag=HT085_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003687194.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00010' for NZ_AP023069.1 Protein Homology CDS 1636 2739 +
dbxref : GenBank:WP_003687195.1,GeneID:66752267
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_003687195.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009174415.1
locus_tag : HT085_RS00010
name : WP_003687195.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-HT085_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_003687195.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344494/working/snpeff_output/NGGayathri/genes.gff' line 14 'NZ_AP023069.1 Protein Homology CDS 1637 2740 . + 0 ID=cds-WP_003687195.1;Parent=gene-HT085_RS00010;Dbxref=GenBank:WP_003687195.1,GeneID:66752267;Name=WP_003687195.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344565/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344565/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'NGGayathri'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NGGayathri'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72344565/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'NGGayathri'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72344565/working/snpeff_output/NGGayathri/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72344565/working/snpeff_output/NGGayathri/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00005' for NZ_AP023069.1 Protein Homology CDS 0 1556 +
dbxref : GenBank:WP_003687194.1,GeneID:66752266
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003687194.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1
locus_tag : HT085_RS00005
name : WP_003687194.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-HT085_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003687194.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344565/working/snpeff_output/NGGayathri/genes.gff' line 12 'NZ_AP023069.1 Protein Homology CDS 1 1557 . + 0 ID=cds-WP_003687194.1;Parent=gene-HT085_RS00005;Dbxref=GenBank:WP_003687194.1,GeneID:66752266;Name=WP_003687194.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1;locus_tag=HT085_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003687194.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00010' for NZ_AP023069.1 Protein Homology CDS 1636 2739 +
dbxref : GenBank:WP_003687195.1,GeneID:66752267
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_003687195.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009174415.1
locus_tag : HT085_RS00010
name : WP_003687195.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-HT085_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_003687195.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344565/working/snpeff_output/NGGayathri/genes.gff' line 14 'NZ_AP023069.1 Protein Homology CDS 1637 2740 . + 0 ID=cds-WP_003687195.1;Parent=gene-HT085_RS00010;Dbxref=GenBank:WP_003687195.1,GeneID:66752267;Name=WP_003687195.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;inference=COORDINATES |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344566/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344566/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Spr'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Spr'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72344566/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Spr'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72344566/working/snpeff_output/Spr/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72344566/working/snpeff_output/Spr/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13125' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13125' for NZ_LN831051.1 Protein Homology CDS 1424 1558 +
dbxref : GenBank:WP_261291558.1,GeneID:93875613
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291558.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13125
name : WP_261291558.1
ontology_term : GO:0006096,GO:0004618
parent : gene-AT689_RS13125
product : phosphoglycerate kinase
protein_id : WP_261291558.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344566/working/snpeff_output/Spr/genes.gff' line 14 'NZ_LN831051.1 Protein Homology CDS 1425 1559 . + 0 ID=cds-WP_261291558.1;Parent=gene-AT689_RS13125;Dbxref=GenBank:WP_261291558.1,GeneID:93875613;Name=WP_261291558.1;Ontology_term=GO:0006096,GO:0004618;gbkey=CDS;gene=pgk;go_function=phosphoglycerate kinase activity|0004618||IEA;go_process=glycolytic process|0006096||IEA;inference=COORDINATES: protein motif:HMM:NF012389.5;locus_tag=AT689_RS13125;product=phosphoglycerate kinase;protein_id=WP_261291558.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13130' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13130' for NZ_LN831051.1 Protein Homology CDS 1587 2075 +
dbxref : GenBank:WP_261291561.1,GeneID:93875614
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291561.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13130
name : WP_261291561.1
ontology_term : GO:0006096,GO:0004618
parent : gene-AT689_RS13130
product : phosphoglycerate kinase
protein_id : WP_261291561.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344566/working/snpeff_output/Spr/genes.gff' line 16 'NZ_LN831051.1 Protein Homology CDS 1588 2076 . + 0 ID=cds-WP_261291561.1;Parent=gene-AT689_RS13130;Dbxref=GenBank:WP_261291561.1,GeneID:93875614;Name=WP_261291561.1;Ontology_term=GO:0006096,GO:0004618;gbkey=CDS;gene=pgk;go_function=phosphoglycerate kinase activity|0004618||IEA;go_process=glycolytic process|0006096||IEA;inference=COORDINATES: protein motif:HMM:NF012389.5;locus_tag=AT689_RS13130;product=phosphoglycerate kinase;protein_id=WP_261291561.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AT689_RS13135' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AT689_RS13135' for NZ_LN831051.1 Protein Homology CDS 1990 2301 +
dbxref : GenBank:WP_261291559.1,GeneID:93875615
gbkey : CDS
gene : pgk
go_function : phosphoglycerate kinase activity|0004618||IEA
go_process : glycolytic process|0006096||IEA
id : cds-WP_261291559.1
inference : COORDINATES: protein motif:HMM:NF012389.5
locus_tag : AT689_RS13135 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344717/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72344717/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'NGGayathri_gff'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NGGayathri_gff'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72344717/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'NGGayathri_gff'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72344717/working/snpeff_output/NGGayathri_gff/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72344717/working/snpeff_output/NGGayathri_gff/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00005' for NZ_AP023069.1 Protein Homology CDS 0 1556 +
dbxref : GenBank:WP_003687194.1,GeneID:66752266
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_003687194.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1
locus_tag : HT085_RS00005
name : WP_003687194.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-HT085_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_003687194.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344717/working/snpeff_output/NGGayathri_gff/genes.gff' line 12 'NZ_AP023069.1 Protein Homology CDS 1 1557 . + 0 ID=cds-WP_003687194.1;Parent=gene-HT085_RS00005;Dbxref=GenBank:WP_003687194.1,GeneID:66752266;Name=WP_003687194.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_002241969.1;locus_tag=HT085_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_003687194.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-HT085_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-HT085_RS00010' for NZ_AP023069.1 Protein Homology CDS 1636 2739 +
dbxref : GenBank:WP_003687195.1,GeneID:66752267
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_003687195.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_009174415.1
locus_tag : HT085_RS00010
name : WP_003687195.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-HT085_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_003687195.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72344717/working/snpeff_output/NGGayathri_gff/genes.gff' line 14 'NZ_AP023069.1 Protein Homology CDS 1637 2740 . + 0 ID=cds-WP_003687195.1;Parent=gene-HT085_RS00010;Dbxref=GenBank:WP_003687195.1,GeneID:66752267;Name=WP_003687195.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|000626 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/347/72347411/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/347/72347411/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'Sta'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/6/8/9/dataset_689b46f0-f986-4c31-b78e-bf5e08aed80b.dat' (line: 1):
CP000253.1 0 2821361 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72347431/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72347431/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonas_aeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonas_aeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72347431/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonas_aeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72347431/working/snpeff_output/Pseudomonas_aeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72347431/working/snpeff_output/Pseudomonas_aeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72347431/working/snpeff_output/Pseudomonas_aeruginosa/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72347431/working/snpeff_output/Pseudomonas_aeruginosa/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72347431/working/snpeff_output/Pseudomonas_aeruginosa/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=c |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72348422/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72348422/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72348422/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Pseudomonasaeruginosa.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72348435/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72348435/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72348435/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72348435/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72348435/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY962_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY962_RS00005' for NZ_RXUH01000001.1 Protein Homology CDS 35 523 -
dbxref : GenBank:WP_003123955.1
gbkey : CDS
gene : phzB
id : cds-WP_003123955.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252900.1
locus_tag : DY962_RS00005
name : WP_003123955.1
parent : gene-DY962_RS00005
product : phenazine biosynthesis protein PhzB
protein_id : WP_003123955.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72348435/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXUH01000001.1 Protein Homology CDS 36 524 . - 0 ID=cds-WP_003123955.1;Parent=gene-DY962_RS00005;Dbxref=GenBank:WP_003123955.1;Name=WP_003123955.1;gbkey=CDS;gene=phzB;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252900.1;locus_tag=DY962_RS00005;product=phenazine biosynthesis protein PhzB;protein_id=WP_003123955.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY962_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY962_RS00010' for NZ_RXUH01000001.1 Protein Homology CDS 553 1041 -
dbxref : GenBank:WP_003114729.1
gbkey : CDS
gene : phzA
id : cds-WP_003114729.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252899.1
locus_tag : DY962_RS00010
name : WP_003114729.1
parent : gene-DY962_RS00010
product : phenazine biosynthesis protein PhzA
protein_id : WP_003114729.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72348435/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXUH01000001.1 Protein Homology CDS 554 1042 . - 0 ID=cds-WP_003114729.1;Parent=gene-DY962_RS00010;Dbxref=GenBank:WP_003114729.1;Name=WP_003114729.1;gbkey=CDS;gene=phzA;inference=COORDINATES: similar to AA sequence:RefSeq:NP_252899.1;locus_tag=DY962_RS00010;product=phenazine biosynthesis protein PhzA;protein_id=WP_003114729.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY962_RS00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY962_RS00020' for NZ_RXUH01000001.1 Protein Homology CDS 1738 2742 +
dbxref : GenBank:WP_003093617.1
gbkey : CDS
gene : phzM
id : cds-WP_003093617.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_252898.1
locus_tag : DY962_RS00020
name : WP_003093617.1
parent : gene-DY962_RS00020
product : phenazine-1-carboxylate N-methyltransferase PhzM
protein_id : WP_003093617.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72348435/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXUH01000001.1 Protein Homology CDS 1739 2743 . + 0 ID=cds-WP_003093617.1;Parent=gene-DY962_RS00020;Dbxref=GenBank:WP_003093617.1;Name=WP_003093617.1;gbkey=CDS;gene=phzM;infe |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72348536/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72348536/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pseudomonasaeruginosa'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pseudomonasaeruginosa'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72348536/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pseudomonasaeruginosa'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72348536/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72348536/working/snpeff_output/Pseudomonasaeruginosa/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY952_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY952_RS00005' for NZ_RXTX01000001.1 Protein Homology CDS 322 3417 -
dbxref : GenBank:WP_096246817.1
gbkey : CDS
gene : dnaE2
id : cds-WP_096246817.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249360.3
locus_tag : DY952_RS00005
name : WP_096246817.1
parent : gene-DY952_RS00005
product : error-prone DNA polymerase
protein_id : WP_096246817.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72348536/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 12 'NZ_RXTX01000001.1 Protein Homology CDS 323 3418 . - 0 ID=cds-WP_096246817.1;Parent=gene-DY952_RS00005;Dbxref=GenBank:WP_096246817.1;Name=WP_096246817.1;gbkey=CDS;gene=dnaE2;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249360.3;locus_tag=DY952_RS00005;product=error-prone DNA polymerase;protein_id=WP_096246817.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY952_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY952_RS00010' for NZ_RXTX01000001.1 Protein Homology CDS 3393 4808 -
dbxref : GenBank:WP_126569722.1
gbkey : CDS
id : cds-WP_126569722.1
inference : COORDINATES: similar to AA sequence:RefSeq:NP_249361.1
locus_tag : DY952_RS00010
name : WP_126569722.1
parent : gene-DY952_RS00010
product : Y-family DNA polymerase
protein_id : WP_126569722.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72348536/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 14 'NZ_RXTX01000001.1 Protein Homology CDS 3394 4809 . - 0 ID=cds-WP_126569722.1;Parent=gene-DY952_RS00010;Dbxref=GenBank:WP_126569722.1;Name=WP_126569722.1;gbkey=CDS;inference=COORDINATES: similar to AA sequence:RefSeq:NP_249361.1;locus_tag=DY952_RS00010;product=Y-family DNA polymerase;protein_id=WP_126569722.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-DY952_RS00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-DY952_RS00015' for NZ_RXTX01000001.1 Protein Homology CDS 4816 5421 -
dbxref : GenBank:WP_031639058.1
gbkey : CDS
gene : imuA
go_process : SOS response|0009432||IEA,negative regulation of cell division|0051782||IEA
id : cds-WP_031639058.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_014820649.1
locus_tag : DY952_RS00015
name : WP_031639058.1
ontology_term : GO:0009432,GO:0051782
parent : gene-DY952_RS00015
product : translesion DNA synthesis-associated protein ImuA
protein_id : WP_031639058.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72348536/working/snpeff_output/Pseudomonasaeruginosa/genes.gff' line 16 'NZ_RXTX01000001.1 Protein Homology CDS 4817 5422 . - 0 ID=cds-WP_031639058.1;Parent=gene-DY952_R |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72349643/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72349643/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72349643/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72349643/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72349643/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72349643/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72349643/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72349721/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72349721/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72349721/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72349721/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72349721/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72349721/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72349721/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350071/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350071/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72350071/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72350071/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72350071/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350071/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350071/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350173/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350173/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72350173/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72350173/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72350173/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350173/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350173/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350429/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350429/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72350429/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72350429/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72350429/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350429/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350429/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350883/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350883/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72350883/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72350883/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72350883/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for NC_003197.2 RefSeq CDS 189 254 +
dbxref : GenBank:NP_459006.1,GeneID:1251519
gbkey : CDS
gene : thrL
id : cds-NP_459006.1
locus_tag : STM0001
name : NP_459006.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : NP_459006.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350883/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'NC_003197.2 RefSeq CDS 190 255 . + 0 ID=cds-NP_459006.1;Parent=gene-STM0001;Dbxref=GenBank:NP_459006.1,GeneID:1251519;Name=NP_459006.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=NP_459006.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for NC_003197.2 RefSeq CDS 336 2798 +
dbxref : GenBank:NP_459007.1,GeneID:1251520
gbkey : CDS
gene : thrA
id : cds-NP_459007.1
locus_tag : STM0002
name : NP_459007.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : NP_459007.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350883/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'NC_003197.2 RefSeq CDS 337 2799 . + 0 ID=cds-NP_459007.1;Parent=gene-STM0002;Dbxref=GenBank:NP_459007.1,GeneID:1251520;Name=NP_459007.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=NP_459007.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for NC_003197.2 RefSeq CDS 2800 3729 +
dbxref : GenBank:NP_459008.1,GeneID:1251521
gbkey : CDS
gene : thrB
id : cds-NP_459008.1
locus_tag : STM0003
name : NP_459008.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_i |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350901/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72350901/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Salmonella_enterica'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Salmonella_enterica'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72350901/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Salmonella_enterica'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72350901/working/snpeff_output/Salmonella_enterica/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72350901/working/snpeff_output/Salmonella_enterica/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for NC_003197.2 RefSeq CDS 189 254 +
dbxref : GenBank:NP_459006.1,GeneID:1251519
gbkey : CDS
gene : thrL
id : cds-NP_459006.1
locus_tag : STM0001
name : NP_459006.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : NP_459006.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350901/working/snpeff_output/Salmonella_enterica/genes.gff' line 10 'NC_003197.2 RefSeq CDS 190 255 . + 0 ID=cds-NP_459006.1;Parent=gene-STM0001;Dbxref=GenBank:NP_459006.1,GeneID:1251519;Name=NP_459006.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=NP_459006.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for NC_003197.2 RefSeq CDS 336 2798 +
dbxref : GenBank:NP_459007.1,GeneID:1251520
gbkey : CDS
gene : thrA
id : cds-NP_459007.1
locus_tag : STM0002
name : NP_459007.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : NP_459007.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72350901/working/snpeff_output/Salmonella_enterica/genes.gff' line 12 'NC_003197.2 RefSeq CDS 337 2799 . + 0 ID=cds-NP_459007.1;Parent=gene-STM0002;Dbxref=GenBank:NP_459007.1,GeneID:1251520;Name=NP_459007.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=NP_459007.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for NC_003197.2 RefSeq CDS 2800 3729 +
dbxref : GenBank:NP_459008.1,GeneID:1251521
gbkey : CDS
gene : thrB
id : cds-NP_459008.1
locus_tag : STM0003
name : NP_459008.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_i |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355650/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355650/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72355650/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72355650/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72355650/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355650/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355650/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355650/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355677/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355677/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72355677/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72355677/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72355677/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355677/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355677/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355677/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355741/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355741/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S.aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S.aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72355741/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S.aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72355741/working/snpeff_output/S.aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72355741/working/snpeff_output/S.aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355741/working/snpeff_output/S.aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355741/working/snpeff_output/S.aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355741/working/snpeff_output/S.aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355851/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72355851/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'S_aereus'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'S_aereus'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72355851/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'S_aereus'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72355851/working/snpeff_output/S_aereus/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72355851/working/snpeff_output/S_aereus/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00001' for NC_007795.1 RefSeq CDS 516 1877 +
dbxref : GenBank:YP_498609.1,GeneID:3919798
gbkey : CDS
gene : dnaA
id : cds-YP_498609.1
locus_tag : SAOUHSC_00001
name : YP_498609.1
note : binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.
parent : gene-SAOUHSC_00001
product : chromosomal replication initiation protein
protein_id : YP_498609.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355851/working/snpeff_output/S_aereus/genes.gff' line 10 'NC_007795.1 RefSeq CDS 517 1878 . + 0 ID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=GenBank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;locus_tag=SAOUHSC_00001;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00002' for NC_007795.1 RefSeq CDS 2155 3288 +
dbxref : GenBank:YP_498610.1,GeneID:3919799
gbkey : CDS
id : cds-YP_498610.1
locus_tag : SAOUHSC_00002
name : YP_498610.1
note : binds the polymerase to DNA and acts as a sliding clamp
parent : gene-SAOUHSC_00002
product : DNA polymerase III subunit beta
protein_id : YP_498610.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355851/working/snpeff_output/S_aereus/genes.gff' line 12 'NC_007795.1 RefSeq CDS 2156 3289 . + 0 ID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=GenBank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;locus_tag=SAOUHSC_00002;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-SAOUHSC_00003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-SAOUHSC_00003' for NC_007795.1 RefSeq CDS 3669 3914 +
dbxref : GenBank:YP_498611.1,GeneID:3919176
gbkey : CDS
id : cds-YP_498611.1
locus_tag : SAOUHSC_00003
name : YP_498611.1
note : conserved hypothetical protein
parent : gene-SAOUHSC_00003
product : hypothetical protein
protein_id : YP_498611.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72355851/working/snpeff_output/S_aereus/genes.gff' line 14 'NC_007795.1 RefSeq CDS 3670 3915 . + 0 ID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=GenBank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserv |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/356/72356945/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/356/72356945/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'S.aereus'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/b/6/6/dataset_b66c797e-a6be-4d35-a8a1-61b0b9aa7c21.dat' (line: 1):
NC_007795.1 0 2821361 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370141/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370141/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCF_000001405.40'
00:00:00 Reading config file: /corral4/main/jobs/072/370/72370141/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GCF_000001405.40.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370148/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370148/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCF_000001405.40'
00:00:00 Reading config file: /corral4/main/jobs/072/370/72370148/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GCF_000001405.40.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370158/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370158/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCF_000001405.40'
00:00:00 Reading config file: /corral4/main/jobs/072/370/72370158/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GCF_000001405.40.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370161/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370161/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCF_000001405.40.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370165/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/370/72370165/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCF000001405.40'
00:00:00 Reading config file: /corral4/main/jobs/072/370/72370165/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GCF000001405.40.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/406/72406798/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/406/72406798/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'h19'
00:00:00 Reading config file: /corral4/main/jobs/072/406/72406798/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'h19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/409/72409859/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/409/72409859/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'athalianaTair10'
00:00:00 Reading config file: /corral4/main/jobs/072/409/72409859/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'athalianaTair10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72415644/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72415644/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: ' GRCh38.105.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72415664/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72415664/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: ' GRCh38.105.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/415/72415734/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/415/72415734/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: ' GRCh38.105.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/415/72415793/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/415/72415793/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: ' GRCh38.105.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/417/72417868/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/417/72417868/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobacterium Tuberculosis H37rv.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72417930/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72417930/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'ASM19595v2.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72418233/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72418233/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'ASM19595v2.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/422/72422832/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/422/72422832/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.p13.RefSeq.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/422/72422979/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/422/72422979/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.13.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423131/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423131/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh37.13'
00:00:00 Reading config file: /corral4/main/jobs/072/423/72423131/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh37.13.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423145/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423145/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh37.p13.RefSeq'
00:00:00 Reading config file: /corral4/main/jobs/072/423/72423145/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh37.p13.RefSeq.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423602/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423602/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh37.115'
00:00:00 Reading config file: /corral4/main/jobs/072/423/72423602/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh37.115.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423647/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/423/72423647/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.115.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438543/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438543/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Arabidopsis_thaliana_TAIR10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438570/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438570/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'TAIR10_chr_all_clean.fasta.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438656/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438656/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Arabidopsis_thaliana_TAIR10'
00:00:00 Reading config file: /corral4/main/jobs/072/438/72438656/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Arabidopsis_thaliana_TAIR10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438673/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/438/72438673/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'athalianaTair10'
00:00:00 Reading config file: /corral4/main/jobs/072/438/72438673/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'athalianaTair10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/439/72439259/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/439/72439259/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Arabidopsis_thaliana_TAIR10'
00:00:00 Reading config file: /corral4/main/jobs/072/439/72439259/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Arabidopsis_thaliana_TAIR10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72446324/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72446324/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Arm_dCD2vdA238L_vaccine'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Arm_dCD2vdA238L_vaccine'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72446324/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Arm_dCD2vdA238L_vaccine'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72446324/working/snpeff_output/Arm_dCD2vdA238L_vaccine/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72446324/working/snpeff_output/Arm_dCD2vdA238L_vaccine/genes.gff'
.00:00:01
Total: 192 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 Reading sequence 'unknown'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-001'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-002'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-003'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-004'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-005'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-006'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-007'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-008'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-009'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Reading sequence 'ArmdCD2vdA238LEnh-010'
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomi |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/455/72455772/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/455/72455772/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Eschericha_coli_str_k_12_susbstr_mq1655.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72456056/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72456056/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Eschericha_coli_str_k_12_susbstr_mq1655'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72456056/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Eschericha_coli_str_k_12_susbstr_mq1655.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/456/72456154/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/456/72456154/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Escherichia_coli_str_k_12_substr_mq1655.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/474/72474273/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/474/72474273/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Athaliana_TAIR10.46'
00:00:00 Reading config file: /corral4/main/jobs/072/474/72474273/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Athaliana_TAIR10.46.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/492/72492316/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/492/72492316/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.36'
00:00:00 Reading config file: /corral4/main/jobs/072/492/72492316/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.36.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72492317/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72492317/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.36'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72492317/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.36.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/492/72492408/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/492/72492408/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.36'
00:00:00 Reading config file: /corral4/main/jobs/072/492/72492408/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.36.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/498/72498859/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/498/72498859/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Athaliana_TAIR10'
00:00:00 Reading config file: /corral4/main/jobs/072/498/72498859/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Athaliana_TAIR10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/518/72518935/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/518/72518935/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'HG19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72533969/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72533969/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'K12'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'K12'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72533969/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'K12'
00:00:01 done
00:00:01 Reading GTF22 data file : '/jetstream2/scratch/main/jobs/72533969/working/snpeff_output/K12/genes.gtf'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72533969/working/snpeff_output/K12/genes.gtf'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_1'. Created transcript 'unassigned_transcript_1' and gene 'ECs_0001' for NC_002695.2 RefSeq CDS 189 269 +
exon_number : 1
gbkey : CDS
gene : thrL
gene_id : ECs_0001
locus_tag : ECs_0001
product : thr operon leader peptide
protein_id : NP_308028.1
transcript_id : unassigned_transcript_1
transl_table : 11
. File '/jetstream2/scratch/main/jobs/72533969/working/snpeff_output/K12/genes.gtf' line 5 'NC_002695.2 RefSeq CDS 190 270 . + 0 gene_id "ECs_0001"; transcript_id "unassigned_transcript_1"; gbkey "CDS"; gene "thrL"; locus_tag "ECs_0001"; product "thr operon leader peptide"; protein_id "NP_308028.1"; transl_table "11"; exon_number "1"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_2'. Created transcript 'unassigned_transcript_2' and gene 'ECs_0002' for NC_002695.2 RefSeq CDS 353 2812 +
exon_number : 1
gbkey : CDS
gene : thrA
gene_id : ECs_0002
locus_tag : ECs_0002
product : aspartokinase I
protein_id : NP_308029.1
transcript_id : unassigned_transcript_2
transl_table : 11
. File '/jetstream2/scratch/main/jobs/72533969/working/snpeff_output/K12/genes.gtf' line 9 'NC_002695.2 RefSeq CDS 354 2813 . + 0 gene_id "ECs_0002"; transcript_id "unassigned_transcript_2"; gbkey "CDS"; gene "thrA"; locus_tag "ECs_0002"; product "aspartokinase I"; protein_id "NP_308029.1"; transl_table "11"; exon_number "1"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_3'. Created transcript 'unassigned_transcript_3' and gene 'ECs_0003' for NC_002695.2 RefSeq CDS 2817 3746 +
exon_number : 1
gbkey : CDS
gene : thrB
gene_id : ECs_0003
locus_tag : ECs_0003
product : homoserine kinase
protein_id : NP_308030.1
transcript_id : unassigned_transcript_3
transl_table : 11
. File '/jetstream2/scratch/main/jobs/72533969/working/snpeff_output/K12/genes.gtf' line 13 'NC_002695.2 RefSeq CDS 2818 3747 . + 0 gene_id "ECs_0003"; transcript_id "unassigned_transcript_3"; gbkey "CDS"; gene "thrB"; locus_tag "ECs_0003"; product "homoserine kinase"; protein_id "NP_308030.1"; transl_table "11"; exon_number "1"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_4'. Created transcript 'unassigned_transcript_4' and gene 'ECs_0004' for NC_002695.2 RefSeq CDS 3750 5033 +
exon_number : 1
gbkey : CDS
gene : thrC
gene_id : ECs_0004
locus_tag : ECs_0004
product : L-threonine synthase
protein_id : NP_308031.1
transcript_id : unassigned_transcript_4
transl_table : 11
. File '/jetstream2/scratch/main/jobs/72533969/working/snpeff_output/K12/genes.gtf' line 17 'NC_002695.2 RefSeq CDS 3751 5034 . + 0 gene_id "ECs_0004"; transcript_id "unassigned_transcript_4"; gbkey "CDS"; gene "thrC"; locus_tag "ECs_0004"; product "L-threonine synthase"; protein_id "NP_308031.1"; transl_table "11"; exon_number "1"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_5'. Create |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72536523/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72536523/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Escherichia_coloi_str_k_12_substr_mg1655'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72536523/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Escherichia_coloi_str_k_12_substr_mg1655.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/536/72536538/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/536/72536538/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Escherichia_coloi_str_k_12_substr_mg1655'
00:00:00 Reading config file: /corral4/main/jobs/072/536/72536538/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Escherichia_coloi_str_k_12_substr_mg1655.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72536543/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72536543/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Escherichia_coloi_str_k_12_substr_mg1655'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72536543/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Escherichia_coloi_str_k_12_substr_mg1655.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/546/72546169/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/546/72546169/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Gavgan'
00:00:00 Reading config file: /corral4/main/jobs/072/546/72546169/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Gavgan.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/548/72548675/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/548/72548675/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/548/72548675/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72559313/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72559313/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'GavganHap2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GavganHap2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72559313/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'GavganHap2'
00:00:01 done
00:00:07 Chromosome: 'CM057589.1' length: 473287416
00:00:07 Create exons from CDS (if needed):
00:00:07 Exons created for 0 transcripts.
00:00:07 Deleting redundant exons (if needed):
00:00:07 Total transcripts with deleted exons: 0
00:00:07 Collapsing zero length introns (if needed):
00:00:07 Total collapsed transcripts: 0
00:00:07 Adding genomic sequences to genes:
00:00:07 Done (0 sequences added).
00:00:07 Adding genomic sequences to exons:
00:00:07 Done (0 sequences added, 0 ignored).
00:00:09 Chromosome: 'CM057590.1' length: 312449569
00:00:09 Create exons from CDS (if needed):
00:00:09 Exons created for 0 transcripts.
00:00:09 Deleting redundant exons (if needed):
00:00:09 Total transcripts with deleted exons: 0
00:00:09 Collapsing zero length introns (if needed):
00:00:09 Total collapsed transcripts: 0
00:00:09 Adding genomic sequences to genes:
00:00:09 Done (0 sequences added).
00:00:09 Adding genomic sequences to exons:
00:00:09 Done (0 sequences added, 0 ignored).
00:00:11 Chromosome: 'CM057591.1' length: 299944300
00:00:11 Create exons from CDS (if needed):
00:00:11 Exons created for 0 transcripts.
00:00:11 Deleting redundant exons (if needed):
00:00:11 Total transcripts with deleted exons: 0
00:00:11 Collapsing zero length introns (if needed):
00:00:11 Total collapsed transcripts: 0
00:00:11 Adding genomic sequences to genes:
00:00:11 Done (0 sequences added).
00:00:11 Adding genomic sequences to exons:
00:00:11 Done (0 sequences added, 0 ignored).
00:00:13 Chromosome: 'CM057592.1' length: 257319116
00:00:13 Create exons from CDS (if needed):
00:00:13 Exons created for 0 transcripts.
00:00:13 Deleting redundant exons (if needed):
00:00:13 Total transcripts with deleted exons: 0
00:00:13 Collapsing zero length introns (if needed):
00:00:13 Total collapsed transcripts: 0
00:00:13 Adding genomic sequences to genes:
00:00:13 Done (0 sequences added).
00:00:13 Adding genomic sequences to exons:
00:00:13 Done (0 sequences added, 0 ignored).
00:00:14 Chromosome: 'CM057593.1' length: 217935827
00:00:14 Create exons from CDS (if needed):
00:00:14 Exons created for 0 transcripts.
00:00:14 Deleting redundant exons (if needed):
00:00:14 Total transcripts with deleted exons: 0
00:00:14 Collapsing zero length introns (if needed):
00:00:14 Total collapsed transcripts: 0
00:00:14 Adding genomic sequences to genes:
00:00:14 Done (0 sequences added).
00:00:14 Adding genomic sequences to exons:
00:00:14 Done (0 sequences added, 0 ignored).
00:00:15 Chromosome: 'CM057594.1' length: 101810359
00:00:15 Create exons from CDS (if needed):
00:00:15 Exons created for 0 transcripts.
00:00:15 Deleting redundant exons (if needed):
00:00:15 Total transcripts with deleted exons: 0
00:00:15 Collapsing zero length introns (if needed):
00:00:15 Total collapsed transcripts: 0
00:00:15 Adding genomic sequences to genes:
00:00:15 Done (0 sequences added).
00:00:15 Adding genomic sequences to exons:
00:00:15 Done (0 sequences a |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/577/72577768/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/577/72577768/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'athalianaTair10_59.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/577/72577828/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/577/72577828/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'athalianaTair10_59'
00:00:00 Reading config file: /corral4/main/jobs/072/577/72577828/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'athalianaTair10_59.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/577/72577859/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/577/72577859/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'araport11.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/600/72600380/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/600/72600380/tmp -Xmx11059m -Xms256m
FATAL ERROR: Failed to download database from [https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testAthalianaTair10.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testAthalianaTair10.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testAthalianaTair10.zip] |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72605606/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72605606/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'testAthalianaTair10'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72605606/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
00:00:01 done
00:00:01 Downloading database for 'testAthalianaTair10'
00:00:01 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testAthalianaTair10.zip' to local file '/jetstream2/scratch/main/jobs/72605606/tmp/snpEff_v5_2_testAthalianaTair10.zip'
00:00:01 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testAthalianaTair10.zip
00:00:01 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testAthalianaTair10.zip, using proxy: false
00:00:02 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testAthalianaTair10.zip
00:00:02 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testAthalianaTair10.zip' to local file '/jetstream2/scratch/main/jobs/72605606/tmp/snpEff_v5_0_testAthalianaTair10.zip'
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testAthalianaTair10.zip
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testAthalianaTair10.zip, using proxy: false
00:00:02 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testAthalianaTair10.zip
00:00:02 Downloading from 'https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testAthalianaTair10.zip' to local file '/jetstream2/scratch/main/jobs/72605606/tmp/snpEff_v5_1_testAthalianaTair10.zip'
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testAthalianaTair10.zip
00:00:02 Connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testAthalianaTair10.zip, using proxy: false
00:00:02 ERROR while connecting to https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testAthalianaTair10.zip
FATAL ERROR: Failed to download database from [https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_testAthalianaTair10.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_testAthalianaTair10.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_testAthalianaTair10.zip] |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/605/72605648/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/605/72605648/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'athaliana130'
00:00:00 Reading config file: /corral4/main/jobs/072/605/72605648/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'athaliana130.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/605/72605686/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/605/72605686/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Arabidopsis_thaliana_TAIR10'
00:00:00 Reading config file: /corral4/main/jobs/072/605/72605686/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Arabidopsis_thaliana_TAIR10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/640/72640878/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/640/72640878/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCF_000182965.3_ASM18296v3'
00:00:00 Reading config file: /corral4/main/jobs/072/640/72640878/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GCF_000182965.3_ASM18296v3.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/641/72641485/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/641/72641485/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Candida albicans ASM18296v2.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/641/72641710/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/641/72641710/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Candida_albicans_SC5314_v2.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/688/72688452/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/688/72688452/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Rev5700snp_Xref._SH5700X.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/688/72688492/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/688/72688492/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Rev5700snp_Xref._SH5700X.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/688/72688854/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/688/72688854/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'SH5700_SnpEff_build.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/689/72689108/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/689/72689108/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'SH5700_SnpEff_build.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/689/72689161/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/689/72689161/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/689/72689213/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/689/72689213/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'SH5700build.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702584/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702584/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SnpEff4.3 Arabidopsis_thaliana'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72702584/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'SnpEff4.3 Arabidopsis_thaliana.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/702/72702617/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/702/72702617/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg19: Homo_sapiens (UCSC)'
00:00:00 Reading config file: /corral4/main/jobs/072/702/72702617/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'hg19: Homo_sapiens (UCSC).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702618/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702618/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'AH_MIC-C_ncbi_2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'AH_MIC-C_ncbi_2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72702618/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Bacterial_and_Plant_Plastid' for genome 'AH_MIC-C_ncbi_2'
00:00:01 done
00:00:02 Chromosome: 'CP005966.1' length: 5024500
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Finishing up genome
00:00:02 Adjusting transcripts:
00:00:02 Adjusting genes:
00:00:02 Adjusting chromosomes lengths:
00:00:02 Ranking exons:
00:00:02 Create UTRs from CDS (if needed):
00:00:02 Remove empty chromosomes:
00:00:02 Marking as 'coding' from CDS information:
00:00:02 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences! |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/702/72702643/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/702/72702643/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg19: Homo_sapiens (UCSC)'
00:00:00 Reading config file: /corral4/main/jobs/072/702/72702643/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'hg19: Homo_sapiens (UCSC).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702697/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702697/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'AH_MIC-C_snps_2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'AH_MIC-C_snps_2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72702697/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Bacterial_and_Plant_Plastid' for genome 'AH_MIC-C_snps_2'
00:00:01 done
00:00:02 Chromosome: 'contig_1' length: 5024500
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Finishing up genome
00:00:02 Adjusting transcripts:
00:00:02 Adjusting genes:
00:00:02 Adjusting chromosomes lengths:
00:00:02 Ranking exons:
00:00:02 Create UTRs from CDS (if needed):
00:00:02 Remove empty chromosomes:
00:00:02 Marking as 'coding' from CDS information:
00:00:02 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences! |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/702/72702755/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/702/72702755/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg19: Homo_sapiens (UCSC)'
00:00:00 Reading config file: /corral4/main/jobs/072/702/72702755/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'hg19: Homo_sapiens (UCSC).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702773/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72702773/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'AH_MIC-C_snps_new'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'AH_MIC-C_snps_new'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72702773/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Bacterial_and_Plant_Plastid' for genome 'AH_MIC-C_snps_new'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72702773/working/snpeff_output/AH_MIC-C_snps_new/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72702773/working/snpeff_output/AH_MIC-C_snps_new/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AHML_00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AHML_00005' for CP005966.1 Genbank CDS 222 1592 +
dbxref : NCBI_GP:AGM41786.1
gbkey : CDS
gene : dnaA
id : cds-AGM41786.1
locus_tag : AHML_00005
name : AGM41786.1
note : COG0593 ATPase involved in DNA replication initiation
parent : gene-AHML_00005
product : chromosomal replication initiation protein
protein_id : AGM41786.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72702773/working/snpeff_output/AH_MIC-C_snps_new/genes.gff' line 8 'CP005966.1 Genbank CDS 223 1593 . + 0 ID=cds-AGM41786.1;Parent=gene-AHML_00005;Dbxref=NCBI_GP:AGM41786.1;Name=AGM41786.1;Note=COG0593 ATPase involved in DNA replication initiation;gbkey=CDS;gene=dnaA;locus_tag=AHML_00005;product=chromosomal replication initiation protein;protein_id=AGM41786.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AHML_00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AHML_00010' for CP005966.1 Genbank CDS 1611 2714 +
dbxref : NCBI_GP:AGM41787.1
gbkey : CDS
id : cds-AGM41787.1
locus_tag : AHML_00010
name : AGM41787.1
note : COG0592 DNA polymerase sliding clamp subunit (PCNA homolog)
parent : gene-AHML_00010
product : DNA polymerase III subunit beta
protein_id : AGM41787.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72702773/working/snpeff_output/AH_MIC-C_snps_new/genes.gff' line 10 'CP005966.1 Genbank CDS 1612 2715 . + 0 ID=cds-AGM41787.1;Parent=gene-AHML_00010;Dbxref=NCBI_GP:AGM41787.1;Name=AGM41787.1;Note=COG0592 DNA polymerase sliding clamp subunit (PCNA homolog);gbkey=CDS;locus_tag=AHML_00010;product=DNA polymerase III subunit beta;protein_id=AGM41787.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AHML_00015' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AHML_00015' for CP005966.1 Genbank CDS 2717 3820 +
dbxref : NCBI_GP:AGM41788.1
gbkey : CDS
id : cds-AGM41788.1
locus_tag : AHML_00015
name : AGM41788.1
note : COG1195 Recombinational DNA repair ATPase (RecF pathway)
parent : gene-AHML_00015
product : DNA replication and repair protein RecF
protein_id : AGM41788.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72702773/working/snpeff_output/AH_MIC-C_snps_new/genes.gff' line 12 'CP005966.1 Genbank CDS 2718 3821 . + 0 ID=cds-AGM41788.1;Parent=gene-AHML_00015;Dbxref=NCBI_GP:AGM41788.1;Name=AGM41788.1;Note=COG1195 Recombinational DNA repair ATPase (RecF pathway);gbkey=CDS;locus_tag=AHML_00015;product=DNA replication and repair protein RecF;protein_id=AGM41788.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-AHML_00020' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-AHML_00020' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72711132/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72711132/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Chromosome1'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Chromosome1'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72711132/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Chromosome1'
00:00:01 done
00:00:07 Chromosome: 'CM000663.2' length: 248956422
00:00:07 Create exons from CDS (if needed):
00:00:07 Exons created for 0 transcripts.
00:00:07 Deleting redundant exons (if needed):
00:00:07 Total transcripts with deleted exons: 0
00:00:07 Collapsing zero length introns (if needed):
00:00:07 Total collapsed transcripts: 0
00:00:07 Adding genomic sequences to genes:
00:00:07 Done (0 sequences added).
00:00:07 Adding genomic sequences to exons:
00:00:07 Done (0 sequences added, 0 ignored).
00:00:07 Finishing up genome
00:00:07 Adjusting transcripts:
00:00:07 Adjusting genes:
00:00:07 Adjusting chromosomes lengths:
00:00:07 Ranking exons:
00:00:07 Create UTRs from CDS (if needed):
00:00:07 Remove empty chromosomes:
00:00:07 Marking as 'coding' from CDS information:
00:00:07 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences! |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712215/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712215/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'FCGR3B'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'FCGR3B'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72712215/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'FCGR3B'
00:00:01 done
00:00:01 Reading GTF22 data file : '/jetstream2/scratch/main/jobs/72712215/working/snpeff_output/FCGR3B/genes.gtf'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72712215/working/snpeff_output/FCGR3B/genes.gtf'
FATAL ERROR: Offending line (lineNum: 2): '1 Ensembl similarity 161624518 161624637 100 - . '
java.lang.ArrayIndexOutOfBoundsException: Index 8 out of bounds for length 8
at org.snpeff.interval.GffMarker.parse(GffMarker.java:284)
at org.snpeff.interval.GffMarker.<init>(GffMarker.java:54)
at org.snpeff.interval.Gtf2Marker.<init>(Gtf2Marker.java:26)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22.parse(SnpEffPredictorFactoryGtf22.java:23)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readGff(SnpEffPredictorFactoryGff.java:529)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:345)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712355/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712355/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'FCGR3B'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'FCGR3B'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72712355/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'FCGR3B'
00:00:01 done
00:00:01 Reading GTF22 data file : '/jetstream2/scratch/main/jobs/72712355/working/snpeff_output/FCGR3B/genes.gtf'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72712355/working/snpeff_output/FCGR3B/genes.gtf'
FATAL ERROR: Offending line (lineNum: 2): '1 Ensembl similarity 161624518 161624637 100 - . '
java.lang.ArrayIndexOutOfBoundsException: Index 8 out of bounds for length 8
at org.snpeff.interval.GffMarker.parse(GffMarker.java:284)
at org.snpeff.interval.GffMarker.<init>(GffMarker.java:54)
at org.snpeff.interval.Gtf2Marker.<init>(Gtf2Marker.java:26)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22.parse(SnpEffPredictorFactoryGtf22.java:23)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readGff(SnpEffPredictorFactoryGff.java:529)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:345)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712528/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712528/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'FCGR3B'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'FCGR3B'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72712528/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'FCGR3B'
00:00:01 done
00:00:01 Reading GTF22 data file : '/jetstream2/scratch/main/jobs/72712528/working/snpeff_output/FCGR3B/genes.gtf'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72712528/working/snpeff_output/FCGR3B/genes.gtf'
FATAL ERROR: Offending line (lineNum: 2): '1 Ensembl similarity 161624518 161624637 100 - . '
java.lang.ArrayIndexOutOfBoundsException: Index 8 out of bounds for length 8
at org.snpeff.interval.GffMarker.parse(GffMarker.java:284)
at org.snpeff.interval.GffMarker.<init>(GffMarker.java:54)
at org.snpeff.interval.Gtf2Marker.<init>(Gtf2Marker.java:26)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22.parse(SnpEffPredictorFactoryGtf22.java:23)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.readGff(SnpEffPredictorFactoryGff.java:529)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff.create(SnpEffPredictorFactoryGff.java:345)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712626/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712626/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'FCGR3B'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'FCGR3B'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72712626/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'FCGR3B'
00:00:02 done
00:00:02 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72712626/working/snpeff_output/FCGR3B/genes.gff'
00:00:02 Reading file '/jetstream2/scratch/main/jobs/72712626/working/snpeff_output/FCGR3B/genes.gff'
..00:00:02
Total: 261 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Reading sequences :
00:00:02 FASTA file: '/jetstream2/scratch/main/jobs/72712626/working/snpeff_output/genomes/FCGR3B.fa' not found.
00:00:02 Reading FASTA file: '/jetstream2/scratch/main/jobs/72712626/working/snpeff_output/FCGR3B/sequences.fa'
00:00:02 Reading sequence 'ENST00000650385.1', length: 2103
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 702
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 122
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 21
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 258
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 258
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 1444
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 666
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 332
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Reading sequence 'ENST00000650385.1', length: 3375
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712631/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72712631/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: '**hg38**.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/720/72720479/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/720/72720479/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'mgdatabase.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/721/72721795/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/721/72721795/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'MG1655db.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/724/72724084/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/724/72724084/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'ce10'
00:00:00 Reading config file: /corral4/main/jobs/072/724/72724084/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'ce10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72741096/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72741096/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Mycobacterium_Tuberculosis.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/782/72782568/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/782/72782568/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/796/72796368/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/796/72796368/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh23.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/796/72796371/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/796/72796371/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh23.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72799462/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72799462/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'FCGR3B4'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'FCGR3B4'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72799462/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'FCGR3B4'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72799462/working/snpeff_output/FCGR3B4/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72799462/working/snpeff_output/FCGR3B4/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_046018.2'. Created transcript 'rna-NR_046018.2' and gene 'GENE_exon-NR_046018.2-1' for NC_000001.11 BestRefSeq EXON 11873 12226 +
dbxref : GeneID:100287102,GenBank:NR_046018.2,HGNC:HGNC:37102
gbkey : misc_RNA
gene : DDX11L1
id : exon-NR_046018.2-1
parent : rna-NR_046018.2
product : DEAD/H-box helicase 11 like 1 (pseudogene)
pseudo : true
source : BestRefSeq
transcript_id : NR_046018.2
type : exon
. File '/jetstream2/scratch/main/jobs/72799462/working/snpeff_output/FCGR3B4/genes.gff' line 9 'NC_000001.11 BestRefSeq exon 11874 12227 . + . ID=exon-NR_046018.2-1;Parent=rna-NR_046018.2;Dbxref=GeneID:100287102,GenBank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1 (pseudogene);pseudo=true;transcript_id=NR_046018.2'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_024540.1'. Created transcript 'rna-NR_024540.1' and gene 'GENE_exon-NR_024540.1-1' for NC_000001.11 BestRefSeq EXON 29320 29369 -
dbxref : GeneID:653635,GenBank:NR_024540.1,HGNC:HGNC:38034
gbkey : misc_RNA
gene : WASH7P
id : exon-NR_024540.1-1
parent : rna-NR_024540.1
product : WASP family homolog 7%2C pseudogene
pseudo : true
source : BestRefSeq
transcript_id : NR_024540.1
type : exon
. File '/jetstream2/scratch/main/jobs/72799462/working/snpeff_output/FCGR3B4/genes.gff' line 14 'NC_000001.11 BestRefSeq exon 29321 29370 . - . ID=exon-NR_024540.1-1;Parent=rna-NR_024540.1;Dbxref=GeneID:653635,GenBank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WASP family homolog 7%2C pseudogene;pseudo=true;transcript_id=NR_024540.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_106918.1'. Created transcript 'rna-NR_106918.1' and gene 'GENE_exon-NR_106918.1-1' for NC_000001.11 BestRefSeq EXON 17368 17435 -
dbxref : GeneID:102466751,GenBank:NR_106918.1,HGNC:HGNC:50039,miRBase:MI0022705
gbkey : precursor_RNA
gene : MIR6859-1
id : exon-NR_106918.1-1
parent : rna-NR_106918.1
product : microRNA 6859-1
source : BestRefSeq
transcript_id : NR_106918.1
type : exon
. File '/jetstream2/scratch/main/jobs/72799462/working/snpeff_output/FCGR3B4/genes.gff' line 27 'NC_000001.11 BestRefSeq exon 17369 17436 . - . ID=exon-NR_106918.1-1;Parent=rna-NR_106918.1;Dbxref=GeneID:102466751,GenBank:NR_106918.1,HGNC:HGNC:50039,miRBase:MI0022705;gbkey=precursor_RNA;gene=MIR6859-1;product=microRNA 6859-1;transcript_id=NR_106918.1'
WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106918.1' (NC_000001.11:17369-17391) does not include 'rna-MIR6859-1-2' (NC_000001.11:17409-17431). Created new gene 'rna-NR_106918.1.2' (NC_000001.11:17409-17431). File '/jetstream2/scratch/main/jobs/72799462/working/snpeff_output/FCGR3B4/genes.gff' line 30 'NC_000001.11 BestRefSeq miRNA 17409 17431 . - . ID=rna-MIR6859-1-2;Parent=rna-NR_106918.1;Dbxref=GeneID:102466751,miRBase:MIMAT0027618,HGNC:HGNC:50039,miRBase:MI0022705;gbkey=ncRNA;gene=MIR6859-1;product=hsa-miR-6859-5p'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcri |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72799544/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72799544/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'FCGR3B4'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'FCGR3B4'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72799544/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'FCGR3B4'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72799544/working/snpeff_output/FCGR3B4/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72799544/working/snpeff_output/FCGR3B4/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_046018.2'. Created transcript 'rna-NR_046018.2' and gene 'GENE_exon-NR_046018.2-1' for NC_000001.11 BestRefSeq EXON 11873 12226 +
dbxref : GeneID:100287102,GenBank:NR_046018.2,HGNC:HGNC:37102
gbkey : misc_RNA
gene : DDX11L1
id : exon-NR_046018.2-1
parent : rna-NR_046018.2
product : DEAD/H-box helicase 11 like 1 (pseudogene)
pseudo : true
source : BestRefSeq
transcript_id : NR_046018.2
type : exon
. File '/jetstream2/scratch/main/jobs/72799544/working/snpeff_output/FCGR3B4/genes.gff' line 9 'NC_000001.11 BestRefSeq exon 11874 12227 . + . ID=exon-NR_046018.2-1;Parent=rna-NR_046018.2;Dbxref=GeneID:100287102,GenBank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1 (pseudogene);pseudo=true;transcript_id=NR_046018.2'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_024540.1'. Created transcript 'rna-NR_024540.1' and gene 'GENE_exon-NR_024540.1-1' for NC_000001.11 BestRefSeq EXON 29320 29369 -
dbxref : GeneID:653635,GenBank:NR_024540.1,HGNC:HGNC:38034
gbkey : misc_RNA
gene : WASH7P
id : exon-NR_024540.1-1
parent : rna-NR_024540.1
product : WASP family homolog 7%2C pseudogene
pseudo : true
source : BestRefSeq
transcript_id : NR_024540.1
type : exon
. File '/jetstream2/scratch/main/jobs/72799544/working/snpeff_output/FCGR3B4/genes.gff' line 14 'NC_000001.11 BestRefSeq exon 29321 29370 . - . ID=exon-NR_024540.1-1;Parent=rna-NR_024540.1;Dbxref=GeneID:653635,GenBank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WASP family homolog 7%2C pseudogene;pseudo=true;transcript_id=NR_024540.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_106918.1'. Created transcript 'rna-NR_106918.1' and gene 'GENE_exon-NR_106918.1-1' for NC_000001.11 BestRefSeq EXON 17368 17435 -
dbxref : GeneID:102466751,GenBank:NR_106918.1,HGNC:HGNC:50039,miRBase:MI0022705
gbkey : precursor_RNA
gene : MIR6859-1
id : exon-NR_106918.1-1
parent : rna-NR_106918.1
product : microRNA 6859-1
source : BestRefSeq
transcript_id : NR_106918.1
type : exon
. File '/jetstream2/scratch/main/jobs/72799544/working/snpeff_output/FCGR3B4/genes.gff' line 27 'NC_000001.11 BestRefSeq exon 17369 17436 . - . ID=exon-NR_106918.1-1;Parent=rna-NR_106918.1;Dbxref=GeneID:102466751,GenBank:NR_106918.1,HGNC:HGNC:50039,miRBase:MI0022705;gbkey=precursor_RNA;gene=MIR6859-1;product=microRNA 6859-1;transcript_id=NR_106918.1'
WARNING_GENE_NOT_FOUND: Gene 'rna-NR_106918.1' (NC_000001.11:17369-17391) does not include 'rna-MIR6859-1-2' (NC_000001.11:17409-17431). Created new gene 'rna-NR_106918.1.2' (NC_000001.11:17409-17431). File '/jetstream2/scratch/main/jobs/72799544/working/snpeff_output/FCGR3B4/genes.gff' line 30 'NC_000001.11 BestRefSeq miRNA 17409 17431 . - . ID=rna-MIR6859-1-2;Parent=rna-NR_106918.1;Dbxref=GeneID:102466751,miRBase:MIMAT0027618,HGNC:HGNC:50039,miRBase:MI0022705;gbkey=ncRNA;gene=MIR6859-1;product=hsa-miR-6859-5p'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcri |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/802/72802420/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/802/72802420/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'R64-1-1.105__tc__Saccharomyces_cerevisiae'
00:00:00 Reading config file: /corral4/main/jobs/072/802/72802420/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'R64-1-1.105__tc__Saccharomyces_cerevisiae.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72802700/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72802700/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Saccharomyces_cerevisiae'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Saccharomyces_cerevisiae'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72802700/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Saccharomyces_cerevisiae'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72802700/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72802700/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL100W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL100W-B' for BK006936.2 tpg CDS 29934 31226 +
dbxref : SGD:S000002149,NCBI_GP:DAA07024.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07024.1
locus_tag : YBL100W-B
name : DAA07024.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL100W-B
product : gag-pol fusion protein
protein_id : DAA07024.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72802700/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 509 'BK006936.2 tpg CDS 29935 31227 . + 0 ID=cds-DAA07024.1;Parent=gene-YBL100W-B;Dbxref=SGD:S000002149,NCBI_GP:DAA07024.1;Name=DAA07024.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL100W-B;product=gag-pol fusion protein;protein_id=DAA07024.1'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL005W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL005W-B' for BK006936.2 tpg CDS 221329 222633 +
dbxref : SGD:S000002147,NCBI_GP:DAA07116.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07116.1
locus_tag : YBL005W-B
name : DAA07116.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL005W-B
product : gag-pol fusion protein
protein_id : DAA07116.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72802700/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 930 'BK006936.2 tpg CDS 221330 222634 . + 0 ID=cds-DAA07116.1;Parent=gene-YBL005W-B;Dbxref=SGD:S000002147,NCBI_GP:DAA07116.1;Name=DAA07116.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72802751/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72802751/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Saccharomyces_cerevisiae'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Saccharomyces_cerevisiae'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72802751/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Saccharomyces_cerevisiae'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72802751/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72802751/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL100W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL100W-B' for BK006936.2 tpg CDS 29934 31226 +
dbxref : SGD:S000002149,NCBI_GP:DAA07024.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07024.1
locus_tag : YBL100W-B
name : DAA07024.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL100W-B
product : gag-pol fusion protein
protein_id : DAA07024.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72802751/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 509 'BK006936.2 tpg CDS 29935 31227 . + 0 ID=cds-DAA07024.1;Parent=gene-YBL100W-B;Dbxref=SGD:S000002149,NCBI_GP:DAA07024.1;Name=DAA07024.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL100W-B;product=gag-pol fusion protein;protein_id=DAA07024.1'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL005W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL005W-B' for BK006936.2 tpg CDS 221329 222633 +
dbxref : SGD:S000002147,NCBI_GP:DAA07116.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07116.1
locus_tag : YBL005W-B
name : DAA07116.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL005W-B
product : gag-pol fusion protein
protein_id : DAA07116.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72802751/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 930 'BK006936.2 tpg CDS 221330 222634 . + 0 ID=cds-DAA07116.1;Parent=gene-YBL005W-B;Dbxref=SGD:S000002147,NCBI_GP:DAA07116.1;Name=DAA07116.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72802939/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72802939/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Saccharomyces_cerevisiae'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Saccharomyces_cerevisiae'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72802939/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Saccharomyces_cerevisiae'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72802939/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72802939/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL100W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL100W-B' for BK006936.2 tpg CDS 29934 31226 +
dbxref : SGD:S000002149,NCBI_GP:DAA07024.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07024.1
locus_tag : YBL100W-B
name : DAA07024.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL100W-B
product : gag-pol fusion protein
protein_id : DAA07024.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72802939/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 509 'BK006936.2 tpg CDS 29935 31227 . + 0 ID=cds-DAA07024.1;Parent=gene-YBL100W-B;Dbxref=SGD:S000002149,NCBI_GP:DAA07024.1;Name=DAA07024.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL100W-B;product=gag-pol fusion protein;protein_id=DAA07024.1'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL005W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL005W-B' for BK006936.2 tpg CDS 221329 222633 +
dbxref : SGD:S000002147,NCBI_GP:DAA07116.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07116.1
locus_tag : YBL005W-B
name : DAA07116.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL005W-B
product : gag-pol fusion protein
protein_id : DAA07116.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72802939/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 930 'BK006936.2 tpg CDS 221330 222634 . + 0 ID=cds-DAA07116.1;Parent=gene-YBL005W-B;Dbxref=SGD:S000002147,NCBI_GP:DAA07116.1;Name=DAA07116.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803007/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803007/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Saccharomyces_cerevisiae'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Saccharomyces_cerevisiae'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72803007/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Saccharomyces_cerevisiae'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72803007/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72803007/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL100W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL100W-B' for BK006936.2 tpg CDS 29934 31226 +
dbxref : SGD:S000002149,NCBI_GP:DAA07024.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07024.1
locus_tag : YBL100W-B
name : DAA07024.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL100W-B
product : gag-pol fusion protein
protein_id : DAA07024.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803007/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 509 'BK006936.2 tpg CDS 29935 31227 . + 0 ID=cds-DAA07024.1;Parent=gene-YBL100W-B;Dbxref=SGD:S000002149,NCBI_GP:DAA07024.1;Name=DAA07024.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL100W-B;product=gag-pol fusion protein;protein_id=DAA07024.1'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL005W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL005W-B' for BK006936.2 tpg CDS 221329 222633 +
dbxref : SGD:S000002147,NCBI_GP:DAA07116.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07116.1
locus_tag : YBL005W-B
name : DAA07116.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL005W-B
product : gag-pol fusion protein
protein_id : DAA07116.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803007/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 930 'BK006936.2 tpg CDS 221330 222634 . + 0 ID=cds-DAA07116.1;Parent=gene-YBL005W-B;Dbxref=SGD:S000002147,NCBI_GP:DAA07116.1;Name=DAA07116.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803045/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803045/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Saccharomyces_cerevisiae'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Saccharomyces_cerevisiae'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72803045/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Saccharomyces_cerevisiae'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72803045/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72803045/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL100W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL100W-B' for BK006936.2 tpg CDS 29934 31226 +
dbxref : SGD:S000002149,NCBI_GP:DAA07024.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07024.1
locus_tag : YBL100W-B
name : DAA07024.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL100W-B
product : gag-pol fusion protein
protein_id : DAA07024.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803045/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 509 'BK006936.2 tpg CDS 29935 31227 . + 0 ID=cds-DAA07024.1;Parent=gene-YBL100W-B;Dbxref=SGD:S000002149,NCBI_GP:DAA07024.1;Name=DAA07024.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL100W-B;product=gag-pol fusion protein;protein_id=DAA07024.1'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL005W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL005W-B' for BK006936.2 tpg CDS 221329 222633 +
dbxref : SGD:S000002147,NCBI_GP:DAA07116.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07116.1
locus_tag : YBL005W-B
name : DAA07116.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL005W-B
product : gag-pol fusion protein
protein_id : DAA07116.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803045/working/snpeff_output/Saccharomyces_cerevisiae/genes.gff' line 930 'BK006936.2 tpg CDS 221330 222634 . + 0 ID=cds-DAA07116.1;Parent=gene-YBL005W-B;Dbxref=SGD:S000002147,NCBI_GP:DAA07116.1;Name=DAA07116.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/803/72803289/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/803/72803289/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'SC'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/6/f/9/dataset_6f91d127-d89a-4586-8c90-b814be9d291c.dat' (line: 1):
BK006935.2 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803407/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803407/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SC_GCF'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SC_GCF'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72803407/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SC_GCF'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72803407/working/snpeff_output/SC_GCF/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72803407/working/snpeff_output/SC_GCF/genes.gff'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL100W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL100W-B' for BK006936.2 tpg CDS 29934 31226 +
dbxref : SGD:S000002149,NCBI_GP:DAA07024.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07024.1
locus_tag : YBL100W-B
name : DAA07024.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL100W-B
product : gag-pol fusion protein
protein_id : DAA07024.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803407/working/snpeff_output/SC_GCF/genes.gff' line 509 'BK006936.2 tpg CDS 29935 31227 . + 0 ID=cds-DAA07024.1;Parent=gene-YBL100W-B;Dbxref=SGD:S000002149,NCBI_GP:DAA07024.1;Name=DAA07024.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL100W-B;product=gag-pol fusion protein;protein_id=DAA07024.1'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL005W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL005W-B' for BK006936.2 tpg CDS 221329 222633 +
dbxref : SGD:S000002147,NCBI_GP:DAA07116.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07116.1
locus_tag : YBL005W-B
name : DAA07116.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL005W-B
product : gag-pol fusion protein
protein_id : DAA07116.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803407/working/snpeff_output/SC_GCF/genes.gff' line 930 'BK006936.2 tpg CDS 221330 222634 . + 0 ID=cds-DAA07116.1;Parent=gene-YBL005W-B;Dbxref=SGD:S000002147,NCBI_GP:DAA07116.1;Name=DAA07116.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL005W-B;product=gag-pol fusion protein;protein_id=DAA07116.1'
.WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-Y |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803538/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72803538/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SC'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SC'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72803538/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SC'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72803538/working/snpeff_output/SC/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72803538/working/snpeff_output/SC/genes.gff'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL100W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL100W-B' for BK006936.2 tpg CDS 29934 31226 +
dbxref : SGD:S000002149,NCBI_GP:DAA07024.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07024.1
locus_tag : YBL100W-B
name : DAA07024.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL100W-B
product : gag-pol fusion protein
protein_id : DAA07024.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803538/working/snpeff_output/SC/genes.gff' line 509 'BK006936.2 tpg CDS 29935 31227 . + 0 ID=cds-DAA07024.1;Parent=gene-YBL100W-B;Dbxref=SGD:S000002149,NCBI_GP:DAA07024.1;Name=DAA07024.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL100W-B;product=gag-pol fusion protein;protein_id=DAA07024.1'
...WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBL005W-B' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-YBL005W-B' for BK006936.2 tpg CDS 221329 222633 +
dbxref : SGD:S000002147,NCBI_GP:DAA07116.1
exception : ribosomal slippage
experiment : EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009]
gbkey : CDS
id : cds-DAA07116.1
locus_tag : YBL005W-B
name : DAA07116.1
note : Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes
parent : gene-YBL005W-B
product : gag-pol fusion protein
protein_id : DAA07116.1
source : tpg
type : CDS
. File '/jetstream2/scratch/main/jobs/72803538/working/snpeff_output/SC/genes.gff' line 930 'BK006936.2 tpg CDS 221330 222634 . + 0 ID=cds-DAA07116.1;Parent=gene-YBL005W-B;Dbxref=SGD:S000002147,NCBI_GP:DAA07116.1;Name=DAA07116.1;Note=Retrotransposon TYA Gag and TYB Pol genes%3B transcribed/translated as one unit%3B polyprotein is processed to make a nucleocapsid-like protein (Gag)%2C reverse transcriptase (RT)%2C protease (PR)%2C and integrase (IN)%3B similar to retroviral genes;exception=ribosomal slippage;experiment=EXISTENCE:direct assay:GO:0005634 nucleus [PMID:9448009];gbkey=CDS;locus_tag=YBL005W-B;product=gag-pol fusion protein;protein_id=DAA07116.1'
.WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-YBR012W-B' is a Gene inst |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/803/72803703/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/803/72803703/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'SC'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/b/9/3/dataset_b9300615-380a-473a-b6a7-7832c2d557c1.dat' (line: 1):
NC_001133.9 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72808199/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72808199/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'C_immitis.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/808/72808813/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/808/72808813/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'C_immitis.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/808/72808895/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/808/72808895/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'C_immitis.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72809082/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72809082/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'C_immitis.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/809/72809394/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/809/72809394/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'C_immitis_custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/809/72809427/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/809/72809427/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'C_immitis_custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72809442/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72809442/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'C_immitis_custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/823/72823675/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/823/72823675/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Lycoris_aurea_chloroplast.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824582/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824582/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'SC'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/0/0/c/dataset_00ca7c0a-9f87-4ecc-bce8-6ff183d89eea.dat' (line: 1):
NC_001133.9 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824592/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824592/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'drojja'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/2/1/2/dataset_212ac0be-e176-4a7f-99c2-2a4346bb2712.dat' (line: 1):
NC_001133.9 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824627/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824627/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'SC'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/0/0/c/dataset_00ca7c0a-9f87-4ecc-bce8-6ff183d89eea.dat' (line: 1):
NC_001133.9 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824678/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824678/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'SC'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/0/0/c/dataset_00ca7c0a-9f87-4ecc-bce8-6ff183d89eea.dat' (line: 1):
NC_001133.9 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824695/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824695/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'SC'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/0/0/c/dataset_00ca7c0a-9f87-4ecc-bce8-6ff183d89eea.dat' (line: 1):
NC_001133.9 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824773/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/824/72824773/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'SC'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/0/0/c/dataset_00ca7c0a-9f87-4ecc-bce8-6ff183d89eea.dat' (line: 1):
NC_001133.9 0 230218 region 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826322/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826322/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826322/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826332/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826332/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826332/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826333/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826333/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826333/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826342/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826342/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826342/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826347/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826347/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826347/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826349/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826349/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826349/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826351/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826351/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826351/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826364/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826364/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826364/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: ' hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826402/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826402/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' hg19'
00:00:00 Reading config file: /corral4/main/jobs/072/826/72826402/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: ' hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826730/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826730/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826732/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826732/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826805/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/826/72826805/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Homo sapiens: hg19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72854578/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72854578/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'papa_cobalt'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'papa_cobalt'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72854578/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'papa_cobalt'
00:00:01 done
00:00:01 Chromosome: 'CP116828.1' length: 2725493
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences! |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72854714/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72854714/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'MGP254'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'MGP254'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72854714/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'MGP254'
00:00:01 done
00:00:01 Chromosome: 'CP116828.1' length: 2725493
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences! |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855135/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855135/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'papa_cobalt.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855136/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855136/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'papa_cobalt.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855137/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855137/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'papa_cobalt.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855138/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/855/72855138/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'papa_cobalt.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72860759/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72860759/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'CD177'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'CD177'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72860759/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'CD177'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72860759/working/snpeff_output/CD177/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72860759/working/snpeff_output/CD177/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_033266.1'. Created transcript 'rna-NR_033266.1' and gene 'GENE_exon-NR_033266.1-1' for NC_000019.10 BestRefSeq EXON 70927 70965 -
dbxref : GeneID:375690,GenBank:NR_033266.1,HGNC:HGNC:33884
gbkey : misc_RNA
gene : WASH5P
id : exon-NR_033266.1-1
parent : rna-NR_033266.1
product : WASP family homolog 5%2C pseudogene
pseudo : true
source : BestRefSeq
transcript_id : NR_033266.1
type : exon
. File '/jetstream2/scratch/main/jobs/72860759/working/snpeff_output/CD177/genes.gff' line 9 'NC_000019.10 BestRefSeq exon 70928 70966 . - . ID=exon-NR_033266.1-1;Parent=rna-NR_033266.1;Dbxref=GeneID:375690,GenBank:NR_033266.1,HGNC:HGNC:33884;gbkey=misc_RNA;gene=WASH5P;product=WASP family homolog 5%2C pseudogene;pseudo=true;transcript_id=NR_033266.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-XR_007067058.1'. Created transcript 'rna-XR_007067058.1' and gene 'GENE_exon-XR_007067058.1-1' for NC_000019.10 Gnomon EXON 71380 72273 +
dbxref : GeneID:105376912,GenBank:XR_007067058.1
gbkey : ncRNA
gene : LOC105376912
id : exon-XR_007067058.1-1
parent : rna-XR_007067058.1
product : uncharacterized LOC105376912
source : Gnomon
transcript_id : XR_007067058.1
type : exon
. File '/jetstream2/scratch/main/jobs/72860759/working/snpeff_output/CD177/genes.gff' line 16 'NC_000019.10 Gnomon exon 71381 72274 . + . ID=exon-XR_007067058.1-1;Parent=rna-XR_007067058.1;Dbxref=GeneID:105376912,GenBank:XR_007067058.1;gbkey=ncRNA;gene=LOC105376912;product=uncharacterized LOC105376912;transcript_id=XR_007067058.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_036268.1'. Created transcript 'rna-NR_036268.1' and gene 'GENE_exon-NR_036268.1-1' for NC_000019.10 BestRefSeq EXON 71972 72109 +
dbxref : GeneID:100422919,GenBank:NR_036268.1,HGNC:HGNC:38246,miRBase:MI0015980
gbkey : precursor_RNA
gene : MIR1302-11
id : exon-NR_036268.1-1
parent : rna-NR_036268.1
product : microRNA 1302-11
source : BestRefSeq
transcript_id : NR_036268.1
type : exon
. File '/jetstream2/scratch/main/jobs/72860759/working/snpeff_output/CD177/genes.gff' line 21 'NC_000019.10 BestRefSeq exon 71973 72110 . + . ID=exon-NR_036268.1-1;Parent=rna-NR_036268.1;Dbxref=GeneID:100422919,GenBank:NR_036268.1,HGNC:HGNC:38246,miRBase:MI0015980;gbkey=precursor_RNA;gene=MIR1302-11;product=microRNA 1302-11;transcript_id=NR_036268.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'rna-NR_026820.1'. Created transcript 'rna-NR_026820.1' and gene 'GENE_exon-NR_026820.1-1' for NC_000019.10 BestRefSeq EXON 77329 77689 -
dbxref : GeneID:641702,GenBank:NR_026820.1,HGNC:HGNC:33581
gbkey : ncRNA
gene : FAM138F
id : exon-NR_026820.1-1
parent : rna-NR_026820.1
product : family with sequence similarity 138 member F
source : BestRefSeq
transcript_id : NR_026820.1
type : exon
. File '/jetstream2/scratch/main/jobs/72860759/working/snpeff_output/CD177/genes.gff' line 26 'NC_000019.10 BestRefSeq exon 77330 77690 . - . ID=exon-NR_026820.1-1;Parent=rna-NR_02 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72861973/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72861973/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'HNA_CD36'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'HNA_CD36'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72861973/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'HNA_CD36'
00:00:01 done
00:00:01 Reading GTF22 data file : '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'NM_001271036.2'. Created transcript 'NM_001271036.2' and gene 'NM_001271036.2' for 1 hg38_ncbiRefSeq STOP_CODON 161624514 161624516 -
gene_id : NM_001271036.2
transcript_id : NM_001271036.2
. File '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf' line 1 'chr1 hg38_ncbiRefSeq stop_codon 161624515 161624517 0.000000 - . gene_id "NM_001271036.2"; transcript_id "NM_001271036.2"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'NM_001271037.2'. Created transcript 'NM_001271037.2' and gene 'NM_001271037.2' for 1 hg38_ncbiRefSeq STOP_CODON 161624514 161624516 -
gene_id : NM_001271037.2
transcript_id : NM_001271037.2
. File '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf' line 12 'chr1 hg38_ncbiRefSeq stop_codon 161624515 161624517 0.000000 - . gene_id "NM_001271037.2"; transcript_id "NM_001271037.2"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'NM_001244753.2'. Created transcript 'NM_001244753.2' and gene 'NM_001244753.2' for 1 hg38_ncbiRefSeq STOP_CODON 161624514 161624516 -
gene_id : NM_001244753.2
transcript_id : NM_001244753.2
. File '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf' line 21 'chr1 hg38_ncbiRefSeq stop_codon 161624515 161624517 0.000000 - . gene_id "NM_001244753.2"; transcript_id "NM_001244753.2"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'NM_001271035.2'. Created transcript 'NM_001271035.2' and gene 'NM_001271035.2' for 1 hg38_ncbiRefSeq STOP_CODON 161624514 161624516 -
gene_id : NM_001271035.2
transcript_id : NM_001271035.2
. File '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf' line 33 'chr1 hg38_ncbiRefSeq stop_codon 161624515 161624517 0.000000 - . gene_id "NM_001271035.2"; transcript_id "NM_001271035.2"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'NM_000570.5'. Created transcript 'NM_000570.5' and gene 'NM_000570.5' for 1 hg38_ncbiRefSeq STOP_CODON 161624514 161624516 -
gene_id : NM_000570.5
transcript_id : NM_000570.5
. File '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf' line 45 'chr1 hg38_ncbiRefSeq stop_codon 161624515 161624517 0.000000 - . gene_id "NM_000570.5"; transcript_id "NM_000570.5"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'NM_020406.4'. Created transcript 'NM_020406.4' and gene 'NM_020406.4' for 19 hg38_ncbiRefSeq START_CODON 43353714 43353716 +
gene_id : NM_020406.4
transcript_id : NM_020406.4
. File '/jetstream2/scratch/main/jobs/72861973/working/snpeff_output/HNA_CD36/genes.gtf' line 58 'chr19 hg38_ncbiRefSeq start_codon 43353715 43353717 0.000000 + . gene_id "NM_020406.4"; transcript_id "NM_020406.4"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'XM_017027022.2'. Created transcript 'XM_017027022.2' and gene 'XM_017027022.2' for 19 hg38_ncbiRefSeq START_CODON 43353714 43353716 +
gene_id : XM_017027022.2
transcript_id : XM_017 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72863552/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72863552/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Database_Salmonella'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Database_Salmonella'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72863552/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Database_Salmonella'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72863552/working/snpeff_output/Database_Salmonella/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72863552/working/snpeff_output/Database_Salmonella/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0001' for AE006468.2 Genbank CDS 189 254 +
dbxref : NCBI_GP:AAL18965.1
gbkey : CDS
gene : thrL
id : cds-AAL18965.1
locus_tag : STM0001
name : AAL18965.1
note : similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21
parent : gene-STM0001
product : thr operon leader peptide
protein_id : AAL18965.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72863552/working/snpeff_output/Database_Salmonella/genes.gff' line 10 'AE006468.2 Genbank CDS 190 255 . + 0 ID=cds-AAL18965.1;Parent=gene-STM0001;Dbxref=NCBI_GP:AAL18965.1;Name=AAL18965.1;Note=similar to E. coli thr operon leader peptide (AAC73112.1)%3B Blastp hit to AAC73112.1 (21 aa)%2C 85-1073758644dentity in aa 1 - 21;gbkey=CDS;gene=thrL;locus_tag=STM0001;product=thr operon leader peptide;protein_id=AAL18965.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0002' for AE006468.2 Genbank CDS 336 2798 +
dbxref : NCBI_GP:AAL18966.1
gbkey : CDS
gene : thrA
id : cds-AAL18966.1
locus_tag : STM0002
name : AAL18966.1
note : bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820
parent : gene-STM0002
product : aspartokinase I
protein_id : AAL18966.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/72863552/working/snpeff_output/Database_Salmonella/genes.gff' line 12 'AE006468.2 Genbank CDS 337 2799 . + 0 ID=cds-AAL18966.1;Parent=gene-STM0002;Dbxref=NCBI_GP:AAL18966.1;Name=AAL18966.1;Note=bifunctional%3B N-terminaus is aspartokinase I and C terminus is homoserine dehydrogenase I%3B similar to E. coli aspartokinase I%2C homoserine dehydrogenase I (AAC73113.1)%3B Blastp hit to AAC73113.1 (820 aa)%2C 94%25 identity in aa 1 - 820;gbkey=CDS;gene=thrA;locus_tag=STM0002;product=aspartokinase I;protein_id=AAL18966.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-STM0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-STM0003' for AE006468.2 Genbank CDS 2800 3729 +
dbxref : NCBI_GP:AAL18967.1
gbkey : CDS
gene : thrB
id : cds-AAL18967.1
locus_tag : STM0003
name : AAL18967.1
note : similar to E. coli homoserine kinase (AAC73114.1)%3B Blastp hit to AAC73114.1 (310 aa)%2C 93%25 identity in aa 1 - 308
parent : gene-STM0003
product : homoserine kinase
protein_id : AAL18967.1
source : Genbank
transl_table : 11
type : CDS
. File '/jetstream |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/868/72868107/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/868/72868107/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/876/72876738/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/876/72876738/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881274/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881274/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'MGP254.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881275/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881275/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'MGP254.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881276/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881276/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'MGP254.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881277/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/881/72881277/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'MGP254.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72888133/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72888133/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'GCA_028540345.1'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GCA_028540345.1'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72888133/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'GCA_028540345.1'
00:00:01 done
00:00:01 Chromosome: 'CP116828.1' length: 2725493
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences! |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72888611/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72888611/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCA_028540345.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/888/72888612/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/888/72888612/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCA_028540345.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/888/72888613/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/888/72888613/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCA_028540345.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/888/72888614/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/888/72888614/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCA_028540345.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72891965/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72891965/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'N2WS235.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/915/72915019/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/915/72915019/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38'
00:00:00 Reading config file: /corral4/main/jobs/072/915/72915019/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/927/72927176/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/927/72927176/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Saccharomyces cerevisiae.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/927/72927255/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/927/72927255/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' GCF_000146045.2 '
00:00:00 Reading config file: /corral4/main/jobs/072/927/72927255/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: ' GCF_000146045.2 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/927/72927272/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/927/72927272/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' Saccharomyces cerevisiae S288C'
00:00:00 Reading config file: /corral4/main/jobs/072/927/72927272/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: ' Saccharomyces cerevisiae S288C.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/939/72939169/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/939/72939169/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'porites lutea'
00:00:00 Reading config file: /corral4/main/jobs/072/939/72939169/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'porites lutea.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/939/72939188/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/939/72939188/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'coral'
00:00:00 Reading config file: /corral4/main/jobs/072/939/72939188/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'coral.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/939/72939443/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/939/72939443/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Exaiptasia diaphana'
00:00:00 Reading config file: /corral4/main/jobs/072/939/72939443/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-2/snpEff.config
java.lang.RuntimeException: Property: 'Exaiptasia diaphana.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72942737/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72942737/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'p45db'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'p45db'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72942737/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'p45db'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72942737/working/snpeff_output/p45db/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72942737/working/snpeff_output/p45db/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XPY37683.1'. Created transcript 'TRANSCRIPT_cds-XPY37683.1' and gene 'GENE_cds-XPY37683.1' for PV167793.1 Genbank CDS 109 588 -
dbxref : NCBI_GP:XPY37683.1
gbkey : CDS
id : cds-XPY37683.1
name : XPY37683.1
note : similar to VACVCP-B15R%3B similar to MYXV M3.1L|R%3B SPPV_001
product : A52R-like family protein
protein_id : XPY37683.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72942737/working/snpeff_output/p45db/genes.gff' line 7 'PV167793.1 Genbank CDS 110 589 . - 0 ID=cds-XPY37683.1;Dbxref=NCBI_GP:XPY37683.1;Name=XPY37683.1;Note=similar to VACVCP-B15R%3B similar to MYXV M3.1L|R%3B SPPV_001;gbkey=CDS;product=A52R-like family protein;protein_id=XPY37683.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XSB36622.1'. Created transcript 'TRANSCRIPT_cds-XSB36622.1' and gene 'GENE_cds-XSB36622.1' for PV167793.1 Genbank CDS 1231 1953 -
dbxref : NCBI_GP:XSB36622.1
gbkey : CDS
id : cds-XSB36622.1
name : XSB36622.1
note : similar to VACVCP-B9R%3B similar to MYXV M-T4-like protein%3B SPPV_003
product : ER-localized apoptosis regulator
protein_id : XSB36622.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72942737/working/snpeff_output/p45db/genes.gff' line 8 'PV167793.1 Genbank CDS 1232 1954 . - 0 ID=cds-XSB36622.1;Dbxref=NCBI_GP:XSB36622.1;Name=XSB36622.1;Note=similar to VACVCP-B9R%3B similar to MYXV M-T4-like protein%3B SPPV_003;gbkey=CDS;product=ER-localized apoptosis regulator;protein_id=XSB36622.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XPY37685.1'. Created transcript 'TRANSCRIPT_cds-XPY37685.1' and gene 'GENE_cds-XPY37685.1' for PV167793.1 Genbank CDS 2242 2748 +
dbxref : NCBI_GP:XPY37685.1
gbkey : CDS
id : cds-XPY37685.1
name : XPY37685.1
note : SPPV_005
product : IL-10-like protein
protein_id : XPY37685.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72942737/working/snpeff_output/p45db/genes.gff' line 9 'PV167793.1 Genbank CDS 2243 2749 . + 0 ID=cds-XPY37685.1;Dbxref=NCBI_GP:XPY37685.1;Name=XPY37685.1;Note=SPPV_005;gbkey=CDS;product=IL-10-like protein;protein_id=XPY37685.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XPY37686.1'. Created transcript 'TRANSCRIPT_cds-XPY37686.1' and gene 'GENE_cds-XPY37686.1' for PV167793.1 Genbank CDS 2759 3454 -
dbxref : NCBI_GP:XPY37686.1
gbkey : CDS
id : cds-XPY37686.1
name : XPY37686.1
note : similar to VACVCP-B16R%3B host defense modulator%3B SPPV_006
product : IL-1-beta-inhibitor
protein_id : XPY37686.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72942737/working/snpeff_output/p45db/genes.gff' line 10 'PV167793.1 Genbank CDS 2760 3455 . - 0 ID=cds-XPY37686.1;Dbxref=NCBI_GP:XPY37686.1;Name=XPY37686.1;Note=similar to VACVCP-B16R%3B host defense modulator%3B SPPV_006;gbkey=CDS;product=IL-1-beta-inhibitor;protein_id=XPY37686.1'
WARNING_TRANSCRIPT_NOT_ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/942/72942895/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/942/72942895/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'p45db.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/942/72942948/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/942/72942948/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'p45db.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72943051/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/72943051/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'SP3db'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SP3db'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/72943051/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'SP3db'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/72943051/working/snpeff_output/SP3db/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/72943051/working/snpeff_output/SP3db/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XPY37683.1'. Created transcript 'TRANSCRIPT_cds-XPY37683.1' and gene 'GENE_cds-XPY37683.1' for PV167793.1 Genbank CDS 109 588 -
dbxref : NCBI_GP:XPY37683.1
gbkey : CDS
id : cds-XPY37683.1
name : XPY37683.1
note : similar to VACVCP-B15R%3B similar to MYXV M3.1L|R%3B SPPV_001
product : A52R-like family protein
protein_id : XPY37683.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72943051/working/snpeff_output/SP3db/genes.gff' line 7 'PV167793.1 Genbank CDS 110 589 . - 0 ID=cds-XPY37683.1;Dbxref=NCBI_GP:XPY37683.1;Name=XPY37683.1;Note=similar to VACVCP-B15R%3B similar to MYXV M3.1L|R%3B SPPV_001;gbkey=CDS;product=A52R-like family protein;protein_id=XPY37683.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XSB36622.1'. Created transcript 'TRANSCRIPT_cds-XSB36622.1' and gene 'GENE_cds-XSB36622.1' for PV167793.1 Genbank CDS 1231 1953 -
dbxref : NCBI_GP:XSB36622.1
gbkey : CDS
id : cds-XSB36622.1
name : XSB36622.1
note : similar to VACVCP-B9R%3B similar to MYXV M-T4-like protein%3B SPPV_003
product : ER-localized apoptosis regulator
protein_id : XSB36622.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72943051/working/snpeff_output/SP3db/genes.gff' line 8 'PV167793.1 Genbank CDS 1232 1954 . - 0 ID=cds-XSB36622.1;Dbxref=NCBI_GP:XSB36622.1;Name=XSB36622.1;Note=similar to VACVCP-B9R%3B similar to MYXV M-T4-like protein%3B SPPV_003;gbkey=CDS;product=ER-localized apoptosis regulator;protein_id=XSB36622.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XPY37685.1'. Created transcript 'TRANSCRIPT_cds-XPY37685.1' and gene 'GENE_cds-XPY37685.1' for PV167793.1 Genbank CDS 2242 2748 +
dbxref : NCBI_GP:XPY37685.1
gbkey : CDS
id : cds-XPY37685.1
name : XPY37685.1
note : SPPV_005
product : IL-10-like protein
protein_id : XPY37685.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72943051/working/snpeff_output/SP3db/genes.gff' line 9 'PV167793.1 Genbank CDS 2243 2749 . + 0 ID=cds-XPY37685.1;Dbxref=NCBI_GP:XPY37685.1;Name=XPY37685.1;Note=SPPV_005;gbkey=CDS;product=IL-10-like protein;protein_id=XPY37685.1'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_cds-XPY37686.1'. Created transcript 'TRANSCRIPT_cds-XPY37686.1' and gene 'GENE_cds-XPY37686.1' for PV167793.1 Genbank CDS 2759 3454 -
dbxref : NCBI_GP:XPY37686.1
gbkey : CDS
id : cds-XPY37686.1
name : XPY37686.1
note : similar to VACVCP-B16R%3B host defense modulator%3B SPPV_006
product : IL-1-beta-inhibitor
protein_id : XPY37686.1
source : Genbank
type : CDS
. File '/jetstream2/scratch/main/jobs/72943051/working/snpeff_output/SP3db/genes.gff' line 10 'PV167793.1 Genbank CDS 2760 3455 . - 0 ID=cds-XPY37686.1;Dbxref=NCBI_GP:XPY37686.1;Name=XPY37686.1;Note=similar to VACVCP-B16R%3B host defense modulator%3B SPPV_006;gbkey=CDS;product=IL-1-beta-inhibitor;protein_id=XPY37686.1'
WARNING_TRANSCRIPT_NOT_ |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/943/72943140/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/943/72943140/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'SP3db.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/965/72965705/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/965/72965705/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'hg38 '
00:00:00 Reading config file: /corral4/main/jobs/072/965/72965705/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'hg38 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/965/72965881/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/072/965/72965881/tmp -Xmx11059m -Xms256m
FATAL ERROR: Failed to download database from [https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_hg38.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_hg38.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_hg38.zip] |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008354/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008354/tmp -Xmx11059m -Xms256m
mv: failed to close '/corral4/main/jobs/073/008/73008354/outputs/dataset_1a6e5ef9-bb50-480e-b9ad-10ddd760dcc2_files/snpeff_stats.genes.txt': Disk quota exceeded |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008356/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008356/tmp -Xmx11059m -Xms256m
FATAL ERROR: Failed to download database from [https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_GRCh37.75.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_GRCh37.75.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_GRCh37.75.zip] |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008372/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008372/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: java.io.IOException: Disk quota exceeded
at org.snpeff.util.Download.unzip(Download.java:374)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:41)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:61)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:110)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1212)
at org.snpeff.SnpEff.loadDb(SnpEff.java:514)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:890)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.io.IOException: Disk quota exceeded
at java.base/java.io.FileDescriptor.close0(Native Method)
at java.base/java.io.FileDescriptor.close(FileDescriptor.java:304)
at java.base/java.io.FileOutputStream$1.close(FileOutputStream.java:407)
at java.base/java.io.FileDescriptor.closeAll(FileDescriptor.java:362)
at java.base/java.io.FileOutputStream.close(FileOutputStream.java:405)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:190)
at org.snpeff.util.Download.unzip(Download.java:357)
... 10 more
java.lang.RuntimeException: Genome download failed!
at org.snpeff.SnpEff.loadDb(SnpEff.java:515)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:890)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008373/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008373/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: java.io.IOException: Disk quota exceeded
at org.snpeff.util.Download.unzip(Download.java:374)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:41)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:61)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:110)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1212)
at org.snpeff.SnpEff.loadDb(SnpEff.java:514)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:890)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.io.IOException: Disk quota exceeded
at java.base/java.io.FileDescriptor.close0(Native Method)
at java.base/java.io.FileDescriptor.close(FileDescriptor.java:304)
at java.base/java.io.FileOutputStream$1.close(FileOutputStream.java:407)
at java.base/java.io.FileDescriptor.closeAll(FileDescriptor.java:362)
at java.base/java.io.FileOutputStream.close(FileOutputStream.java:405)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:190)
at org.snpeff.util.Download.unzip(Download.java:357)
... 10 more
java.lang.RuntimeException: Genome download failed!
at org.snpeff.SnpEff.loadDb(SnpEff.java:515)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:890)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008374/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008374/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: java.io.IOException: Disk quota exceeded
at org.snpeff.util.Download.unzip(Download.java:374)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:41)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:61)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:110)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1212)
at org.snpeff.SnpEff.loadDb(SnpEff.java:514)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:890)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.io.IOException: Disk quota exceeded
at java.base/java.io.FileDescriptor.close0(Native Method)
at java.base/java.io.FileDescriptor.close(FileDescriptor.java:304)
at java.base/java.io.FileOutputStream$1.close(FileOutputStream.java:407)
at java.base/java.io.FileDescriptor.closeAll(FileDescriptor.java:362)
at java.base/java.io.FileOutputStream.close(FileOutputStream.java:405)
at java.base/java.io.FilterOutputStream.close(FilterOutputStream.java:190)
at org.snpeff.util.Download.unzip(Download.java:357)
... 10 more
java.lang.RuntimeException: Genome download failed!
at org.snpeff.SnpEff.loadDb(SnpEff.java:515)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:890)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008375/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008375/tmp -Xmx11059m -Xms256m
FATAL ERROR: Failed to download database from [https://snpeff.odsp.astrazeneca.com/databases/v5_2/snpEff_v5_2_GRCh37.75.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_0/snpEff_v5_0_GRCh37.75.zip, https://snpeff.odsp.astrazeneca.com/databases/v5_1/snpEff_v5_1_GRCh37.75.zip] |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008610/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008610/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008611/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008611/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008612/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008612/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008613/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008613/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008614/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008614/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008615/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008615/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008616/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008616/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008617/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008617/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008618/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008618/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008620/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008620/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008621/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008621/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008623/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008623/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008624/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008624/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008625/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008625/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008626/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008626/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008627/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008627/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008628/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008628/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008629/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008629/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008630/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008630/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008631/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008631/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008632/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008632/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008633/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008633/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008634/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008634/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008635/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008635/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008636/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008636/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008637/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008637/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008638/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008638/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008639/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008639/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008640/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008640/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008642/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008642/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008643/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/008/73008643/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008644/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73008644/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/022/73022875/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/022/73022875/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'ce11 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/022/73022928/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/022/73022928/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'ce11.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/023/73023635/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/023/73023635/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p14 '
00:00:00 Reading config file: /corral4/main/jobs/073/023/73023635/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.p14 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73025691/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73025691/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Etenella_Houghton_pEimTen1'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Etenella_Houghton_pEimTen1'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73025691/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Etenella_Houghton_pEimTen1'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73025691/working/snpeff_output/Etenella_Houghton_pEimTen1/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73025691/working/snpeff_output/Etenella_Houghton_pEimTen1/genes.gff'
....................................................................................................
10000 ....................................................................................................
20000 ....................................................................................................
30000 ....................................................................................................
40000 ....................................................................................................
50000 ....................................................................................................
60000 ........................00:00:02
Total: 62458 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:03 Total collapsed transcripts: 0
00:00:03 Reading sequences :
00:00:03 FASTA file: '/jetstream2/scratch/main/jobs/73025691/working/snpeff_output/genomes/Etenella_Houghton_pEimTen1.fa' not found.
00:00:03 Reading FASTA file: '/jetstream2/scratch/main/jobs/73025691/working/snpeff_output/Etenella_Houghton_pEimTen1/sequences.fa'
00:00:03 Reading sequence 'ENA|HG994971|HG994971.1', length: 4218128
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'ENA|HG994963|HG994963.1', length: 1819161
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'ENA|HG994966|HG994966.1', length: 3367513
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'ENA|HG994961|HG994961.1', length: 998389
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'ENA|HG994969|HG994969.1', length: 3854180
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'ENA|HG994977|HG994977.1', length: 34753
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'ENA|HG994962|HG994962.1', length: 1151236
00:00:0 |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031211/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031211/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031212/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031212/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031213/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031213/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031214/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031214/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031215/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031215/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031216/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031216/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031217/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031217/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031218/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031218/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031219/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031219/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031220/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031220/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031221/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031221/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031222/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031222/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031223/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031223/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031224/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031224/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031225/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031225/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031226/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031226/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031227/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031227/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031228/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031228/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031229/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031229/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031230/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031230/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | /jetstream2/scratch/main/jobs/73031231/tool_script.sh: line 24: /jetstream2/scratch/main/jobs/730Show full stderr/jetstream2/scratch/main/jobs/73031231/tool_script.sh: line 24: /jetstream2/scratch/main/jobs/73031231/working/: Is a directory |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031232/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031232/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031233/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031233/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031234/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031234/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031235/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031235/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031236/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031236/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031237/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031237/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031238/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031238/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031239/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031239/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031240/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031240/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031241/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031241/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031242/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031242/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031243/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031243/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031244/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031244/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031245/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031245/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031246/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/031/73031246/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/043/73043334/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/043/73043334/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p14 '
00:00:00 Reading config file: /corral4/main/jobs/073/043/73043334/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.p14 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73046263/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73046263/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'tmprss6'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'tmprss6'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73046263/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'tmprss6'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73046263/working/snpeff_output/tmprss6/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73046263/working/snpeff_output/tmprss6/genes.gff'
........00:00:01
Total: 885 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/73046263/working/snpeff_output/genomes/tmprss6.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/73046263/working/snpeff_output/tmprss6/sequences.fa'
00:00:01 Reading sequence 'NC_000022.11:c37110536-37065436', length: 45101
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
.
0 00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
There might be differences in the chromosome names used in the genes file ('/jetstream2/scratch/main/jobs/73046263/working/snpeff_output/tmprss6/genes.gff')
and the chromosme names used in the 'reference sequence' file.
Please check that chromosome names in both files match.
Chromosome names missing in 'reference sequence' file: '22'
Chromosome names missing in 'genes' file : 'NC_000022.11:c37110536-37065436' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/062/73062159/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/062/73062159/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh36.105.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/072/73072360/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/072/73072360/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Escherichia_coli_K-12'
00:00:00 Reading config file: /corral4/main/jobs/073/072/73072360/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'Escherichia_coli_K-12.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:03 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073705/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073705/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073706/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073706/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073707/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073707/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073708/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073708/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073709/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073709/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073710/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073710/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073711/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073711/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073712/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073712/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073713/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073713/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073714/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073714/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073715/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073715/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073716/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073716/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073717/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073717/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073718/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073718/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073719/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073719/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073720/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073720/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073721/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073721/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073722/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073722/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073723/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073723/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073724/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073724/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073725/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073725/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073726/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073726/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073727/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073727/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073728/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073728/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073729/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073729/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073730/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073730/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073731/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073731/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073732/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073732/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073733/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073733/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073734/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073734/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073735/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073735/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073736/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073736/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073737/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073737/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073738/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073738/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073739/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/073/73073739/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/074/73074117/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/074/73074117/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCH38.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73076205/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73076205/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Ecoli'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Ecoli'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73076205/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Ecoli'
00:00:01 done
00:00:01 Reading GTF22 data file : '/jetstream2/scratch/main/jobs/73076205/working/snpeff_output/Ecoli/genes.gtf'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73076205/working/snpeff_output/Ecoli/genes.gtf'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_1'. Created transcript 'unassigned_transcript_1' and gene 'b0001' for NC_000913.3 RefSeq CDS 189 251 +
db_xref : GeneID:944742
exon_number : 1
gbkey : CDS
gene : thrL
gene_id : b0001
locus_tag : b0001
product : thr operon leader peptide
protein_id : NP_414542.1
transcript_id : unassigned_transcript_1
transl_table : 11
. File '/jetstream2/scratch/main/jobs/73076205/working/snpeff_output/Ecoli/genes.gtf' line 5 'NC_000913.3 RefSeq CDS 190 252 . + 0 gene_id "b0001"; transcript_id "unassigned_transcript_1"; db_xref "UniProtKB/Swiss-Prot:P0AD86"; db_xref "GenBank:NP_414542.1"; db_xref "ASAP:ABE-0000006"; db_xref "ECOCYC:EG11277"; db_xref "GeneID:944742"; gbkey "CDS"; gene "thrL"; locus_tag "b0001"; product "thr operon leader peptide"; protein_id "NP_414542.1"; transl_table "11"; exon_number "1"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_2'. Created transcript 'unassigned_transcript_2' and gene 'b0002' for NC_000913.3 RefSeq CDS 336 2795 +
db_xref : GeneID:945803
exon_number : 1
gbkey : CDS
gene : thrA
gene_id : b0002
locus_tag : b0002
product : fused aspartate kinase/homoserine dehydrogenase 1
protein_id : NP_414543.1
transcript_id : unassigned_transcript_2
transl_table : 11
. File '/jetstream2/scratch/main/jobs/73076205/working/snpeff_output/Ecoli/genes.gtf' line 9 'NC_000913.3 RefSeq CDS 337 2796 . + 0 gene_id "b0002"; transcript_id "unassigned_transcript_2"; db_xref "UniProtKB/Swiss-Prot:P00561"; db_xref "GenBank:NP_414543.1"; db_xref "ASAP:ABE-0000008"; db_xref "ECOCYC:EG10998"; db_xref "GeneID:945803"; gbkey "CDS"; gene "thrA"; locus_tag "b0002"; product "fused aspartate kinase/homoserine dehydrogenase 1"; protein_id "NP_414543.1"; transl_table "11"; exon_number "1"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_3'. Created transcript 'unassigned_transcript_3' and gene 'b0003' for NC_000913.3 RefSeq CDS 2800 3729 +
db_xref : GeneID:947498
exon_number : 1
gbkey : CDS
gene : thrB
gene_id : b0003
locus_tag : b0003
product : homoserine kinase
protein_id : NP_414544.1
transcript_id : unassigned_transcript_3
transl_table : 11
. File '/jetstream2/scratch/main/jobs/73076205/working/snpeff_output/Ecoli/genes.gtf' line 13 'NC_000913.3 RefSeq CDS 2801 3730 . + 0 gene_id "b0003"; transcript_id "unassigned_transcript_3"; db_xref "UniProtKB/Swiss-Prot:P00547"; db_xref "GenBank:NP_414544.1"; db_xref "ASAP:ABE-0000010"; db_xref "ECOCYC:EG10999"; db_xref "GeneID:947498"; gbkey "CDS"; gene "thrB"; locus_tag "b0003"; product "homoserine kinase"; protein_id "NP_414544.1"; transl_table "11"; exon_number "1"; '
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'unassigned_transcript_4'. Created transcript 'unassigned_transcript_4' and gene 'b0004' for NC_000913.3 RefSeq CDS 3733 5016 +
db_xref : GeneID:945198
exon_number : 1
gbkey : CDS
gene : th |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/078/73078072/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/078/73078072/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084763/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084763/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'ecoli12'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'ecoli12'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73084763/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'ecoli12'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73084763/working/snpeff_output/ecoli12/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73084763/working/snpeff_output/ecoli12/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0001' for NC_000913.3 RefSeq CDS 189 254 +
dbxref : UniProtKB/Swiss-Prot:P0AD86,GenBank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,GeneID:944742
gbkey : CDS
gene : thrL
id : cds-NP_414542.1
locus_tag : b0001
name : NP_414542.1
parent : gene-b0001
product : thr operon leader peptide
protein_id : NP_414542.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73084763/working/snpeff_output/ecoli12/genes.gff' line 10 'NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds-NP_414542.1;Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,GenBank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;gene=thrL;locus_tag=b0001;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0002' for NC_000913.3 RefSeq CDS 336 2798 +
dbxref : UniProtKB/Swiss-Prot:P00561,GenBank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,GeneID:945803
gbkey : CDS
gene : thrA
id : cds-NP_414543.1
locus_tag : b0002
name : NP_414543.1
parent : gene-b0002
product : fused aspartate kinase/homoserine dehydrogenase 1
protein_id : NP_414543.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73084763/working/snpeff_output/ecoli12/genes.gff' line 12 'NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds-NP_414543.1;Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,GenBank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;gene=thrA;locus_tag=b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0003' for NC_000913.3 RefSeq CDS 2800 3732 +
dbxref : UniProtKB/Swiss-Prot:P00547,GenBank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,GeneID:947498
gbkey : CDS
gene : thrB
id : cds-NP_414544.1
locus_tag : b0003
name : NP_414544.1
parent : gene-b0003
product : homoserine kinase
protein_id : NP_414544.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73084763/working/snpeff_output/ecoli12/genes.gff' line 14 'NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds-NP_414544.1;Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,GenBank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;gene=thrB;locus_tag=b0003;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0004' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0004' for NC_000913.3 RefSeq CDS 3733 5019 +
dbxref : UniProtKB/Swiss-Prot:P00934,GenBank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,GeneID:945198
gbkey : CDS |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084774/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084774/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'E.coli'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'E.coli'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73084774/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'E.coli'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73084774/working/snpeff_output/E.coli/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73084774/working/snpeff_output/E.coli/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0001' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0001' for NC_000913.3 RefSeq CDS 189 254 +
dbxref : UniProtKB/Swiss-Prot:P0AD86,GenBank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,GeneID:944742
gbkey : CDS
gene : thrL
id : cds-NP_414542.1
locus_tag : b0001
name : NP_414542.1
parent : gene-b0001
product : thr operon leader peptide
protein_id : NP_414542.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73084774/working/snpeff_output/E.coli/genes.gff' line 10 'NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds-NP_414542.1;Parent=gene-b0001;Dbxref=UniProtKB/Swiss-Prot:P0AD86,GenBank:NP_414542.1,ASAP:ABE-0000006,ECOCYC:EG11277,GeneID:944742;Name=NP_414542.1;gbkey=CDS;gene=thrL;locus_tag=b0001;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0002' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0002' for NC_000913.3 RefSeq CDS 336 2798 +
dbxref : UniProtKB/Swiss-Prot:P00561,GenBank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,GeneID:945803
gbkey : CDS
gene : thrA
id : cds-NP_414543.1
locus_tag : b0002
name : NP_414543.1
parent : gene-b0002
product : fused aspartate kinase/homoserine dehydrogenase 1
protein_id : NP_414543.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73084774/working/snpeff_output/E.coli/genes.gff' line 12 'NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds-NP_414543.1;Parent=gene-b0002;Dbxref=UniProtKB/Swiss-Prot:P00561,GenBank:NP_414543.1,ASAP:ABE-0000008,ECOCYC:EG10998,GeneID:945803;Name=NP_414543.1;gbkey=CDS;gene=thrA;locus_tag=b0002;product=fused aspartate kinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0003' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0003' for NC_000913.3 RefSeq CDS 2800 3732 +
dbxref : UniProtKB/Swiss-Prot:P00547,GenBank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,GeneID:947498
gbkey : CDS
gene : thrB
id : cds-NP_414544.1
locus_tag : b0003
name : NP_414544.1
parent : gene-b0003
product : homoserine kinase
protein_id : NP_414544.1
source : RefSeq
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73084774/working/snpeff_output/E.coli/genes.gff' line 14 'NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds-NP_414544.1;Parent=gene-b0003;Dbxref=UniProtKB/Swiss-Prot:P00547,GenBank:NP_414544.1,ASAP:ABE-0000010,ECOCYC:EG10999,GeneID:947498;Name=NP_414544.1;gbkey=CDS;gene=thrB;locus_tag=b0003;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-b0004' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-b0004' for NC_000913.3 RefSeq CDS 3733 5019 +
dbxref : UniProtKB/Swiss-Prot:P00934,GenBank:NP_414545.1,ASAP:ABE-0000012,ECOCYC:EG11000,GeneID:945198
gbkey : CDS
gene |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084821/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084821/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'ecoli'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'ecoli'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73084821/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'ecoli'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73084821/working/snpeff_output/ecoli/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73084821/working/snpeff_output/ecoli/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/73084821/working/snpeff_output/genomes/ecoli.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/73084821/working/snpeff_output/ecoli/sequences.fa'
00:00:01 Reading sequence 'NC_000913.3', length: 4641458
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'NC_000913.3' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084850/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73084850/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'E.coli'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'E.coli'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73084850/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'E.coli'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73084850/working/snpeff_output/E.coli/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73084850/working/snpeff_output/E.coli/genes.gff'
00:00:01 Total: 0 markers added.
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Reading sequences :
00:00:01 FASTA file: '/jetstream2/scratch/main/jobs/73084850/working/snpeff_output/genomes/E.coli.fa' not found.
00:00:01 Reading FASTA file: '/jetstream2/scratch/main/jobs/73084850/working/snpeff_output/E.coli/sequences.fa'
00:00:01 Reading sequence 'NC_000913.3', length: 4641591
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Total: 0 sequences added, 0 sequences ignored.
00:00:01 Finishing up genome
00:00:01 Adjusting transcripts:
00:00:01 Adjusting genes:
00:00:01 Adjusting chromosomes lengths:
00:00:01 Ranking exons:
00:00:01 Create UTRs from CDS (if needed):
00:00:01 Correcting exons based on frame information.
00:00:01
00:00:01 Remove empty chromosomes:
00:00:01 Marking as 'coding' from CDS information:
00:00:01 Done: 0 transcripts marked
FATAL ERROR: Most Exons do not have sequences!
Chromosome names missing in 'genes' file : 'NC_000913.3' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/086/73086480/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/086/73086480/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Plasmodium falciparum '
00:00:00 Reading config file: /corral4/main/jobs/073/086/73086480/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'Plasmodium falciparum .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/105/73105284/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/105/73105284/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.14.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73118323/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73118323/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Pf'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Pf'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73118323/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Pf'
00:00:01 done
00:00:01 Reading GTF22 data file : '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf'
..............WARNING_GENE_NOT_FOUND: Gene 'PF3D7_1440200' (NC_037283.1:1639477-1641760) does not include 'XM_001348520.2' (NC_037283.1:1639477-1647167). Created new gene 'PF3D7_1440200.2' (NC_037283.1:1639477-1647167). File '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf' line 3231 'NC_037283.1 ncbiRefSeq.2024-10-03 transcript 1639477 1647167 . + . gene_id "PF3D7_1440200"; transcript_id "XM_001348520.2"; gene_name "PF3D7_1440200";'
.......WARNING_GENE_NOT_FOUND: Gene 'PF3D7_1419800.1' (NC_037283.1:822423-824202) does not include 'XM_024473355.1' (NC_037283.1:822423-824340). Created new gene 'PF3D7_1419800.1.2' (NC_037283.1:822423-824340). File '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf' line 4900 'NC_037283.1 ncbiRefSeq.2024-10-03 transcript 822423 824340 . - . gene_id "PF3D7_1419800.1"; transcript_id "XM_024473355.1"; gene_name "PF3D7_1419800.1";'
...WARNING_GENE_NOT_FOUND: Gene 'PF3D7_1412900.1' (NC_037283.1:521209-522242) does not include 'XM_001348265.1' (NC_037283.1:521209-522898). Created new gene 'PF3D7_1412900.1.2' (NC_037283.1:521209-522898). File '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf' line 5474 'NC_037283.1 ncbiRefSeq.2024-10-03 transcript 521209 522898 . + . gene_id "PF3D7_1412900.1"; transcript_id "XM_001348265.1"; gene_name "PF3D7_1412900.1";'
...WARNING_GENE_NOT_FOUND: Gene 'PF3D7_1404600.1' (NC_037283.1:154855-158855) does not include 'XM_024473342.1' (NC_037283.1:154855-159595). Created new gene 'PF3D7_1404600.1.2' (NC_037283.1:154855-159595). File '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf' line 6178 'NC_037283.1 ncbiRefSeq.2024-10-03 transcript 154855 159595 . - . gene_id "PF3D7_1404600.1"; transcript_id "XM_024473342.1"; gene_name "PF3D7_1404600.1";'
WARNING_GENE_NOT_FOUND: Gene 'PF3D7_1404600.1' (NC_037283.1:154855-158855) does not include 'XM_024473340.1' (NC_037283.1:154855-160191). Created new gene 'PF3D7_1404600.1.3' (NC_037283.1:154855-160191). File '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf' line 6221 'NC_037283.1 ncbiRefSeq.2024-10-03 transcript 154855 160191 . - . gene_id "PF3D7_1404600.1"; transcript_id "XM_024473340.1"; gene_name "PF3D7_1404600.1";'
......WARNING_GENE_NOT_FOUND: Gene 'PF3D7_1361500.1' (NC_004331.3:2467128-2467982) does not include 'XM_002809049.1' (NC_004331.3:2465491-2467982). Created new gene 'PF3D7_1361500.1.2' (NC_004331.3:2465491-2467982). File '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/genes.gtf' line 7455 'NC_004331.3 ncbiRefSeq.2024-10-03 transcript 2465491 2467982 . - . gene_id "PF3D7_1361500.1"; transcript_id "XM_002809049.1"; gene_name "PF3D7_1361500.1";'
....................WARNING_GENE_NOT_FOUND: Gene 'PF3D7_1304200.1' (NC_004331.3:226669-228290) does not include 'XM_002808950.1' (NC_004331.3:226669-228873). Created new gene 'PF3D7_1304200.1.2' (NC_004331.3:226669-228873). File '/jetstream2/scratch/main/jobs/73118323/working/snpeff_output/Pf/gene |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130823/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130823/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Pf.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130824/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130824/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Pf.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130825/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130825/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Pf.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130826/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/130/73130826/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Pf.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/161/73161034/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/161/73161034/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Hom sapiens: hg3822 '
00:00:00 Reading config file: /corral4/main/jobs/073/161/73161034/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'Hom sapiens: hg3822 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/161/73161061/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/161/73161061/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg3822 '
00:00:00 Reading config file: /corral4/main/jobs/073/161/73161061/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg3822 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/161/73161079/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/161/73161079/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens: hg38 22 '
00:00:00 Reading config file: /corral4/main/jobs/073/161/73161079/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens: hg38 22 .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/165/73165898/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/165/73165898/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.86) .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167827/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167827/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167828/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167828/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167829/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167829/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167830/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167830/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167831/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167831/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167832/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167832/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167833/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167833/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167834/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/167/73167834/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCm38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73176781/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73176781/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'pig-chr7'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'pig-chr7'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73176781/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'pig-chr7'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'transcript:ENSSSCT00000041166'. File '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff' line 19 '7 ensembl five_prime_UTR 43487 43666 . + . Parent=transcript:ENSSSCT00000041166'
WARNING_CANNOT_ADD_UTR: Could not add UTR. File '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff' line 19 '7 ensembl five_prime_UTR 43487 43666 . + . Parent=transcript:ENSSSCT00000041166'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'transcript:ENSSSCT00000041166'. Created transcript 'transcript:ENSSSCT00000041166' and gene 'GENE_ENSSSCE00000367588' for 7 ensembl EXON 43486 43686 +
constitutive : 0
ensembl_end_phase : 0
ensembl_phase : -1
exon_id : ENSSSCE00000367588
name : ENSSSCE00000367588
parent : transcript:ENSSSCT00000041166
rank : 1
source : ensembl
type : exon
version : 3
. File '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff' line 20 '7 ensembl exon 43487 43687 . + . Parent=transcript:ENSSSCT00000041166;Name=ENSSSCE00000367588;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=ENSSSCE00000367588;rank=1;version=3'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'transcript:ENSSSCT00000044982'. File '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff' line 38 '7 ensembl five_prime_UTR 43598 43666 . + . Parent=transcript:ENSSSCT00000044982'
WARNING_CANNOT_ADD_UTR: Could not add UTR. File '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff' line 38 '7 ensembl five_prime_UTR 43598 43666 . + . Parent=transcript:ENSSSCT00000044982'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'transcript:ENSSSCT00000044982'. Created transcript 'transcript:ENSSSCT00000044982' and gene 'GENE_ENSSSCE00000296677' for 7 ensembl EXON 43597 43686 +
constitutive : 0
ensembl_end_phase : 0
ensembl_phase : -1
exon_id : ENSSSCE00000296677
name : ENSSSCE00000296677
parent : transcript:ENSSSCT00000044982
rank : 1
source : ensembl
type : exon
version : 2
. File '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff' line 39 '7 ensembl exon 43598 43687 . + . Parent=transcript:ENSSSCT00000044982;Name=ENSSSCE00000296677;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=ENSSSCE00000296677;rank=1;version=2'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'transcript:ENSSSCT00000105559'. Created transcript 'transcript:ENSSSCT00000105559' and gene 'GENE_ENSSSCE00000502366' for 7 ensembl EXON 87359 87448 +
constitutive : 0
ensembl_end_phase : -1
ensembl_phase : -1
exon_id : ENSSSCE00000502366
name : ENSSSCE00000502366
parent : transcript:ENSSSCT00000105559
rank : 1
source : ensembl
type : exon
version : 1
. File '/jetstream2/scratch/main/jobs/73176781/working/snpeff_output/pig-chr7/genes.gff' line 59 '7 ensembl exon 87360 87449 . + . Parent=transcript:ENSSSCT00000105559;Name=ENSSSCE00000502366;constitutive=0;ensembl_end_phase=-1;ensem |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/199/73199769/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/199/73199769/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'human_mitochondrial'
00:00:00 Reading config file: /corral4/main/jobs/073/199/73199769/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'human_mitochondrial.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/199/73199886/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/199/73199886/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Bifidobacterium longum.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/200/73200062/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/200/73200062/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' testHg19ChrM'
00:00:00 Reading config file: /corral4/main/jobs/073/200/73200062/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: ' testHg19ChrM.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/200/73200077/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/200/73200077/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' testHg19ChrM '
00:00:00 Reading config file: /corral4/main/jobs/073/200/73200077/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: ' testHg19ChrM .genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/200/73200120/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/200/73200120/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'testHg19ChrM.genome'
00:00:00 Reading config file: /corral4/main/jobs/073/200/73200120/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'testHg19ChrM.genome.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73201625/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73201625/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'B_longum_Custom'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'B_longum_Custom'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73201625/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'B_longum_Custom'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73201625/working/snpeff_output/B_longum_Custom/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73201625/working/snpeff_output/B_longum_Custom/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-BLLJ_RS00005' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-BLLJ_RS00005' for NC_015067.1 Protein Homology CDS 0 1502 +
dbxref : GenBank:WP_007051767.1,GeneID:69577253
gbkey : CDS
gene : dnaA
go_function : DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA
go_process : DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA
id : cds-WP_007051767.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_003827867.1
locus_tag : BLLJ_RS00005
name : WP_007051767.1
ontology_term : GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524
parent : gene-BLLJ_RS00005
product : chromosomal replication initiator protein DnaA
protein_id : WP_007051767.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73201625/working/snpeff_output/B_longum_Custom/genes.gff' line 8 'NC_015067.1 Protein Homology CDS 1 1503 . + 0 ID=cds-WP_007051767.1;Parent=gene-BLLJ_RS00005;Dbxref=GenBank:WP_007051767.1,GeneID:69577253;Name=WP_007051767.1;Ontology_term=GO:0006270,GO:0006275,GO:0003677,GO:0003688,GO:0005524;gbkey=CDS;gene=dnaA;go_function=DNA binding|0003677||IEA,DNA replication origin binding|0003688||IEA,ATP binding|0005524||IEA;go_process=DNA replication initiation|0006270||IEA,regulation of DNA replication|0006275||IEA;inference=COORDINATES: similar to AA sequence:RefSeq:WP_003827867.1;locus_tag=BLLJ_RS00005;product=chromosomal replication initiator protein DnaA;protein_id=WP_007051767.1;transl_table=11'
WARNING_TRANSCRIPT_NOT_FOUND: Exon's parent 'gene-BLLJ_RS00010' is a Gene instead of a transcript. Created transcript 'TRANSCRIPT_gene-BLLJ_RS00010' for NC_015067.1 Protein Homology CDS 2238 3362 +
dbxref : GenBank:WP_007051765.1,GeneID:69577254
gbkey : CDS
gene : dnaN
go_component : DNA polymerase III complex|0009360||IEA
go_function : DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA
go_process : DNA replication|0006260||IEA
id : cds-WP_007051765.1
inference : COORDINATES: similar to AA sequence:RefSeq:WP_007051765.1
locus_tag : BLLJ_RS00010
name : WP_007051765.1
ontology_term : GO:0006260,GO:0003677,GO:0003887,GO:0009360
parent : gene-BLLJ_RS00010
product : DNA polymerase III subunit beta
protein_id : WP_007051765.1
source : Protein Homology
transl_table : 11
type : CDS
. File '/jetstream2/scratch/main/jobs/73201625/working/snpeff_output/B_longum_Custom/genes.gff' line 10 'NC_015067.1 Protein Homology CDS 2239 3363 . + 0 ID=cds-WP_007051765.1;Parent=gene-BLLJ_RS00010;Dbxref=GenBank:WP_007051765.1,GeneID:69577254;Name=WP_007051765.1;Ontology_term=GO:0006260,GO:0003677,GO:0003887,GO:0009360;gbkey=CDS;gene=dnaN;go_component=DNA polymerase III complex|0009360||IEA;go_function=DNA binding|0003677||IEA,DNA-directed DNA polymerase activity|0003887||IEA;go_process=DNA replication|0006260||IEA;infere |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73201829/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73201829/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Ab10'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Ab10'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73201829/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Ab10'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73201829/working/snpeff_output/Ab10/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73201829/working/snpeff_output/Ab10/genes.gff'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_fig|6666666.963977.peg.1'. Created transcript 'TRANSCRIPT_fig|6666666.963977.peg.1' and gene 'GENE_fig|6666666.963977.peg.1' for Ab_10_merged_10N FIG CDS 231 1118 -
id : fig|6666666.963977.peg.1
name : hypothetical protein
source : FIG
type : CDS
. File '/jetstream2/scratch/main/jobs/73201829/working/snpeff_output/Ab10/genes.gff' line 2 'Ab_10_merged_10N FIG CDS 232 1119 . - 1 ID=fig|6666666.963977.peg.1;Name=hypothetical protein'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_fig|6666666.963977.peg.2'. Created transcript 'TRANSCRIPT_fig|6666666.963977.peg.2' and gene 'GENE_fig|6666666.963977.peg.2' for Ab_10_merged_10N FIG CDS 1137 1970 -
id : fig|6666666.963977.peg.2
name : CDP-diacylglycerol--serine O-phosphatidyltransferase (EC 2.7.8.8) @ Archaetidylserine synthase (EC 2.7.8.38)
ontology_term : KEGG_ENZYME:2.7.8.8,KEGG_ENZYME:2.7.8.38
source : FIG
type : CDS
. File '/jetstream2/scratch/main/jobs/73201829/working/snpeff_output/Ab10/genes.gff' line 3 'Ab_10_merged_10N FIG CDS 1138 1971 . - 1 ID=fig|6666666.963977.peg.2;Name=CDP-diacylglycerol--serine O-phosphatidyltransferase (EC 2.7.8.8) @ Archaetidylserine synthase (EC 2.7.8.38);Ontology_term=KEGG_ENZYME:2.7.8.8,KEGG_ENZYME:2.7.8.38'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_fig|6666666.963977.peg.3'. Created transcript 'TRANSCRIPT_fig|6666666.963977.peg.3' and gene 'GENE_fig|6666666.963977.peg.3' for Ab_10_merged_10N FIG CDS 2012 2869 -
id : fig|6666666.963977.peg.3
name : 23S rRNA (adenine(2030)-N(6))-methyltransferase (EC 2.1.1.266)
ontology_term : KEGG_ENZYME:2.1.1.266
source : FIG
type : CDS
. File '/jetstream2/scratch/main/jobs/73201829/working/snpeff_output/Ab10/genes.gff' line 4 'Ab_10_merged_10N FIG CDS 2013 2870 . - 0 ID=fig|6666666.963977.peg.3;Name=23S rRNA (adenine(2030)-N(6))-methyltransferase (EC 2.1.1.266);Ontology_term=KEGG_ENZYME:2.1.1.266'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_fig|6666666.963977.peg.4'. Created transcript 'TRANSCRIPT_fig|6666666.963977.peg.4' and gene 'GENE_fig|6666666.963977.peg.4' for Ab_10_merged_10N FIG CDS 2987 3592 +
id : fig|6666666.963977.peg.4
name : SM-20-related protein
source : FIG
type : CDS
. File '/jetstream2/scratch/main/jobs/73201829/working/snpeff_output/Ab10/genes.gff' line 5 'Ab_10_merged_10N FIG CDS 2988 3593 . + 0 ID=fig|6666666.963977.peg.4;Name=SM-20-related protein'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript 'TRANSCRIPT_fig|6666666.963977.peg.5'. Created transcript 'TRANSCRIPT_fig|6666666.963977.peg.5' and gene 'GENE_fig|6666666.963977.peg.5' for Ab_10_merged_10N FIG CDS 3660 4187 +
id : fig|6666666.963977.peg.5
name : hypothetical protein
source : FIG
type : CDS
. File '/jetstream2/scratch/main/jobs/73201829/working/snpeff_output/Ab10/genes.gff' line 6 'Ab_10_merged_10N FIG CDS 3661 4188 . + 1 ID=fig|6666666.963977.peg.5;Name=hypothetical protein'
WARNING_TRANSCRIPT_NOT_FOUND: Cannot find transcript |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202027/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202027/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202072/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202072/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202134/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202134/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202206/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202206/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202470/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202470/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202616/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/202/73202616/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh37'
00:00:00 Reading config file: /corral4/main/jobs/073/202/73202616/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73206068/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73206068/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Ecolk12'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Ecolk12'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73206068/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Ecolk12'
00:00:01 done
Gpr.reader(521): java.util.zip.ZipException: Not in GZIP format
Gpr.reader(521): java.util.zip.ZipException: Not in GZIP format
00:00:01 No sequence found in feature file.
00:00:01 Trying fasta file '/jetstream2/scratch/main/jobs/73206068/working/snpeff_output/genomes/Ecolk12.fa'
00:00:01 Trying fasta file '/jetstream2/scratch/main/jobs/73206068/working/snpeff_output/Ecolk12/sequences.fa'
java.lang.RuntimeException: Cannot find sequence for 'Ecolk12'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.sequence(SnpEffPredictorFactoryFeatures.java:533)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addFeatures(SnpEffPredictorFactoryFeatures.java:95)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:351)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
java.lang.RuntimeException: Error reading file '/jetstream2/scratch/main/jobs/73206068/working/snpeff_output/Ecolk12/genes.gbk'
java.lang.RuntimeException: Cannot find sequence for 'Ecolk12'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:365)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73207062/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73207062/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'coli'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'coli'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73207062/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'coli'
00:00:01 done
Gpr.reader(521): java.util.zip.ZipException: Not in GZIP format
Gpr.reader(521): java.util.zip.ZipException: Not in GZIP format
00:00:01 No sequence found in feature file.
00:00:01 Trying fasta file '/jetstream2/scratch/main/jobs/73207062/working/snpeff_output/genomes/coli.fa'
00:00:01 Trying fasta file '/jetstream2/scratch/main/jobs/73207062/working/snpeff_output/coli/sequences.fa'
java.lang.RuntimeException: Cannot find sequence for 'coli'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.sequence(SnpEffPredictorFactoryFeatures.java:533)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.addFeatures(SnpEffPredictorFactoryFeatures.java:95)
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:351)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
java.lang.RuntimeException: Error reading file '/jetstream2/scratch/main/jobs/73207062/working/snpeff_output/coli/genes.gbk'
java.lang.RuntimeException: Cannot find sequence for 'coli'
at org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures.create(SnpEffPredictorFactoryFeatures.java:365)
at org.snpeff.snpEffect.commandLine.SnpEffCmdBuild.run(SnpEffCmdBuild.java:414)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/209/73209336/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/209/73209336/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/209/73209746/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/209/73209746/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/209/73209959/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/209/73209959/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210330/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210330/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210621/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210621/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Bifidobacterium.longum.NC_015067.1'
00:00:00 Reading config file: /corral4/main/jobs/073/210/73210621/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'Bifidobacterium.longum.NC_015067.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:03 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210758/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210758/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NC_015067.1'
00:00:00 Reading config file: /corral4/main/jobs/073/210/73210758/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'NC_015067.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210870/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/210/73210870/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'B_longum_Custom.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/215/73215640/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/215/73215640/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/222/73222874/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/222/73222874/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'S.Typhimurium_V2.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/242/73242906/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/242/73242906/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCH38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/242/73242963/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/242/73242963/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'h19'
00:00:00 Reading config file: /corral4/main/jobs/073/242/73242963/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'h19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/247/73247701/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/247/73247701/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/249/73249606/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/249/73249606/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/273/73273615/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/273/73273615/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/273/73273616/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/273/73273616/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/285/73285249/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/285/73285249/tmp -Xmx11059m -Xms256m
FATAL ERROR: No transcripts left for analysis after filter using file '/corral4/main/objects/0/7/5/dataset_075f8adf-0168-466b-b759-266e0d8788ec.dat' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/285/73285462/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/285/73285462/tmp -Xmx11059m -Xms256m
FATAL ERROR: No transcripts left for analysis after filter using file '/corral4/main/objects/a/3/d/dataset_a3d9a3f1-8796-4a22-9fc5-376d40fe9f22.dat' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/286/73286498/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/286/73286498/tmp -Xmx11059m -Xms256m
FATAL ERROR: No transcripts left for analysis after filter using file '/corral4/main/objects/d/5/d/dataset_d5d4f374-52f5-4548-9554-921a30818088.dat' |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73295827/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73295827/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73295827/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Etenella_Houghton_pEimTen1_2'
00:00:01 done
00:00:01 Chromosome: 'HG994961.1' length: 998389
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Chromosome: 'HG994962.1' length: 1151236
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:02 Chromosome: 'HG994963.1' length: 1819161
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Chromosome: 'HG994964.1' length: 1948711
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Chromosome: 'HG994965.1' length: 2810749
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Chromosome: 'HG994966.1' length: 3367513
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to e |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297174/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297174/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297175/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297175/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297205/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297205/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'grch38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297206/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297206/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'grch38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297249/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297249/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'grch38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297340/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/297/73297340/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73301524/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73301524/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73301524/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Etenella_Houghton_pEimTen1_2'
00:00:01 done
00:00:01 Chromosome: 'HG994961.1' length: 998389
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Chromosome: 'HG994962.1' length: 1151236
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:01 Chromosome: 'HG994963.1' length: 1819161
00:00:01 Create exons from CDS (if needed):
00:00:01 Exons created for 0 transcripts.
00:00:01 Deleting redundant exons (if needed):
00:00:01 Total transcripts with deleted exons: 0
00:00:01 Collapsing zero length introns (if needed):
00:00:01 Total collapsed transcripts: 0
00:00:01 Adding genomic sequences to genes:
00:00:01 Done (0 sequences added).
00:00:01 Adding genomic sequences to exons:
00:00:01 Done (0 sequences added, 0 ignored).
00:00:02 Chromosome: 'HG994964.1' length: 1948711
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Chromosome: 'HG994965.1' length: 2810749
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to exons:
00:00:02 Done (0 sequences added, 0 ignored).
00:00:02 Chromosome: 'HG994966.1' length: 3367513
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:02 Total collapsed transcripts: 0
00:00:02 Adding genomic sequences to genes:
00:00:02 Done (0 sequences added).
00:00:02 Adding genomic sequences to e |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/318/73318109/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/318/73318109/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/324/73324802/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/324/73324802/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'at org.snpeff.snpEffect.EffectType.parse(Eff.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/330/73330051/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/330/73330051/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: ' GRCh38.86'
00:00:00 Reading config file: /corral4/main/jobs/073/330/73330051/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: ' GRCh38.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73332466/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73332466/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Grch38.86'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73332466/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'Grch38.86.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:00 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/342/73342847/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/342/73342847/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38'
00:00:00 Reading config file: /corral4/main/jobs/073/342/73342847/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/342/73342869/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/342/73342869/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p13.genome'
00:00:00 Reading config file: /corral4/main/jobs/073/342/73342869/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'GRCh38.p13.genome.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73342886/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73342886/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'database.clinvar.GRCh38'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73342886/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'database.clinvar.GRCh38.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/349/73349693/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/349/73349693/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/349/73349710/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/349/73349710/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/349/73349730/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/349/73349730/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'HG19.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73349755/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73349755/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73349755/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Etenella_Houghton_pEimTen1_2'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73349755/working/snpeff_output/Etenella_Houghton_pEimTen1_2/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73349755/working/snpeff_output/Etenella_Houghton_pEimTen1_2/genes.gff'
....................................................................................................
10000 ....................................................................................................
20000 ....................................................................................................
30000 ....................................................................................................
40000 ....................................................................................................
50000 ....................................................................................................
60000 ........................00:00:02
Total: 62458 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:03 Total transcripts with deleted exons: 0
00:00:03 Collapsing zero length introns (if needed):
00:00:03 Total collapsed transcripts: 0
00:00:03 Reading sequences :
00:00:03 FASTA file: '/jetstream2/scratch/main/jobs/73349755/working/snpeff_output/genomes/Etenella_Houghton_pEimTen1_2.fa' not found.
00:00:03 Reading FASTA file: '/jetstream2/scratch/main/jobs/73349755/working/snpeff_output/Etenella_Houghton_pEimTen1_2/sequences.fa'
00:00:03 Reading sequence 'HG994961.1', length: 998389
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994962.1', length: 1151236
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994963.1', length: 1819161
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994964.1', length: 1948711
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994965.1', length: 2810749
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994966.1', length: 3367513
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994967.1', length: 3616812
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequence |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73349789/tmp -Xmx44237m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73349789/tmp -Xmx44237m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'build'
00:00:00 Building database for 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Etenella_Houghton_pEimTen1_2'
00:00:00 Reading config file: /jetstream2/scratch/main/jobs/73349789/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-1/snpEff.config
00:00:01 Codon table 'Standard' for genome 'Etenella_Houghton_pEimTen1_2'
00:00:01 done
00:00:01 Reading GFF3 data file : '/jetstream2/scratch/main/jobs/73349789/working/snpeff_output/Etenella_Houghton_pEimTen1_2/genes.gff'
00:00:01 Reading file '/jetstream2/scratch/main/jobs/73349789/working/snpeff_output/Etenella_Houghton_pEimTen1_2/genes.gff'
....................................................................................................
10000 ....................................................................................................
20000 ....................................................................................................
30000 ....................................................................................................
40000 ....................................................................................................
50000 ....................................................................................................
60000 ........................00:00:02
Total: 62458 markers added.
00:00:02 Create exons from CDS (if needed):
00:00:02 Exons created for 0 transcripts.
00:00:02 Deleting redundant exons (if needed):
00:00:02 Total transcripts with deleted exons: 0
00:00:02 Collapsing zero length introns (if needed):
00:00:03 Total collapsed transcripts: 0
00:00:03 Reading sequences :
00:00:03 FASTA file: '/jetstream2/scratch/main/jobs/73349789/working/snpeff_output/genomes/Etenella_Houghton_pEimTen1_2.fa' not found.
00:00:03 Reading FASTA file: '/jetstream2/scratch/main/jobs/73349789/working/snpeff_output/Etenella_Houghton_pEimTen1_2/sequences.fa'
00:00:03 Reading sequence 'HG994961.1', length: 998389
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994962.1', length: 1151236
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994963.1', length: 1819161
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994964.1', length: 1948711
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994965.1', length: 2810749
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994966.1', length: 3367513
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequences added).
00:00:03 Adding genomic sequences to exons:
00:00:03 Done (0 sequences added, 0 ignored).
00:00:03 Reading sequence 'HG994967.1', length: 3616812
00:00:03 Adding genomic sequences to genes:
00:00:03 Done (0 sequence |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/353/73353441/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/353/73353441/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'TAIR10.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/365/73365241/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/365/73365241/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'CriGri-PICRH-1.0.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/365/73365248/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/365/73365248/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCF_003668045.3.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/367/73367568/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/367/73367568/tmp -Xmx11059m -Xms256m
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/8/4/e/dataset_84e69bb9-2a94-48f6-a7b0-a2d068eb347c.dat' (line: 1):
chrI 1 C . 1
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '1'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '1'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/367/73367640/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/367/73367640/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'SacCer_Apr2011.18.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/369/73369203/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/369/73369203/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'CriGri'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/b/d/d/dataset_bdd55230-d351-4105-91fc-8e4ec3bd4cfb.dat' (line: 2):
NC_048595.1,88901,.,A,G,.,PASS,11,0,0,1,0,1/1,29,11,11,0,6,100%,1.08E-03,0,34,0,0,3,3
java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
NC_048595.1,88901,.,A,G,.,PASS,11,0,0,1,0,1/1,29,11,11,0,6,100%,1.08E-03,0,34,0,0,3,3
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
NC_048595.1,88901,.,A,G,.,PASS,11,0,0,1,0,1/1,29,11,11,0,6,100%,1.08E-03,0,34,0,0,3,3
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1035)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/369/73369293/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/369/73369293/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome 'CriGri'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/7/c/e/dataset_7ce4d87d-b71c-45aa-bb46-9d317dae373f.dat' (line: 1):
NC_048595.1,88901,.,A,G,.,PASS,11,0,0,1,0,1/1,29,11,11,0,6,100%,1.08E-03,0,34,0,0,3,3
java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
NC_048595.1,88901,.,A,G,.,PASS,11,0,0,1,0,1/1,29,11,11,0,6,100%,1.08E-03,0,34,0,0,3,3
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
NC_048595.1,88901,.,A,G,.,PASS,11,0,0,1,0,1/1,29,11,11,0,6,100%,1.08E-03,0,34,0,0,3,3
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1035)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/371/73371433/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/371/73371433/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'candida auris'
00:00:00 Reading config file: /corral4/main/jobs/073/371/73371433/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'candida auris.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/376/73376625/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/376/73376625/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'dbNSFP'
00:00:00 Reading config file: /corral4/main/jobs/073/376/73376625/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'dbNSFP.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/376/73376889/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/376/73376889/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh37'
00:00:00 Reading config file: /corral4/main/jobs/073/376/73376889/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-5/snpEff.config
java.lang.RuntimeException: Property: 'GRCh37.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:00 Logging
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/376/73376899/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/376/73376899/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'Homo sapiens (GRCh37.75)'
00:00:00 Reading config file: /corral4/main/jobs/073/376/73376899/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-5/snpEff.config
java.lang.RuntimeException: Property: 'Homo sapiens (GRCh37.75).genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:00 Logging
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/377/73377700/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/377/73377700/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRCh37.5'
00:00:00 Reading config file: /corral4/main/jobs/073/377/73377700/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-4.3.1t-5/snpEff.config
java.lang.RuntimeException: Property: 'GRCh37.5.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:106)
at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
at org.snpeff.snpEffect.Config.init(Config.java:480)
at org.snpeff.snpEffect.Config.<init>(Config.java:117)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
00:00:01 Logging
00:00:02 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/382/73382471/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/382/73382471/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRch37.75'
00:00:00 Reading config file: /corral4/main/jobs/073/382/73382471/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'GRch37.75.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/382/73382600/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/382/73382600/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'GRch37.75'
00:00:00 Reading config file: /corral4/main/jobs/073/382/73382600/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'GRch37.75.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/397/73397829/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/397/73397829/tmp -Xmx11059m -Xms256m
VcfFileIterator.parseVcfLine(132): Fatal error reading file '/corral4/main/objects/e/0/d/dataset_e0da9841-a177-4570-bedd-a9e3d660b73d.dat' (line: 2):
erreur initiale
java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
erreur initiale
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:133)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:184)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:57)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:467)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:142)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1029)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
erreur initiale
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1007)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:219)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:130)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/397/73397959/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/397/73397959/tmp -Xmx11059m -Xms256m
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/corral4/main/objects/e/0/d/dataset_e0da9841-a177-4570-bedd-a9e3d660b73d.dat' (line: 2):
erreur initiale
java.lang.RuntimeException: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
erreur initiale
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: Impropper VCF entry: Not enough fields (missing tab separators?).
erreur initiale
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1035)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/398/73398081/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/398/73398081/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'Phytophthora_mt.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/401/73401638/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/401/73401638/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCF_001457635.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73401793/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73401793/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCF_001457635.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/405/73405092/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/405/73405092/tmp -Xmx11059m -Xms256m
java.lang.RuntimeException: Property: 'GCF_001457635.1.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163) |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/407/73407583/tmp -Xmx11059m -XShow full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/corral4/main/jobs/073/407/73407583/tmp -Xmx11059m -Xms256m
00:00:00 SnpEff version SnpEff 5.2 (build 2023-09-29 06:17), by Pablo Cingolani
00:00:00 Command: 'download'
00:00:00 Reading configuration file 'snpEff.config'. Genome: 'SnpEff5.2'
00:00:00 Reading config file: /corral4/main/jobs/073/407/73407583/working/snpEff.config
00:00:00 Reading config file: /usr/local/share/snpeff-5.2-3/snpEff.config
java.lang.RuntimeException: Property: 'SnpEff5.2.genome' not found
at org.snpeff.interval.Genome.<init>(Genome.java:103)
at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
at org.snpeff.snpEffect.Config.init(Config.java:532)
at org.snpeff.snpEffect.Config.<init>(Config.java:119)
at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:105)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:97)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
00:00:01 Done. |
| 1 | Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73416553/tmp -Xmx11059m Show full stderrPicked up _JAVA_OPTIONS: -Djava.io.tmpdir=/jetstream2/scratch/main/jobs/73416553/tmp -Xmx11059m -Xms256m
00:00:00 Codon table 'Standard' for genome '207-27'
VcfFileIterator.parseVcfLine(133): Fatal error reading file '/jetstream2/scratch/main/jobs/73416553/inputs/dataset_94298ab4-d079-472d-9bf7-abeb73df758b.dat' (line: 1):
Chr1 0 1350 CDS 0 +
java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:134)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:185)
at org.snpeff.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:58)
at org.snpeff.fileIterator.FileIterator.hasNext(FileIterator.java:123)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotateVcf(SnpEffCmdEff.java:473)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.annotate(SnpEffCmdEff.java:139)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:918)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
at org.snpeff.SnpEff.run(SnpEff.java:1173)
at org.snpeff.SnpEff.main(SnpEff.java:163)
Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '0'
at org.snpeff.vcf.VcfEntry.parseAltSingle(VcfEntry.java:1169)
at org.snpeff.vcf.VcfEntry.parseAlts(VcfEntry.java:1044)
at org.snpeff.vcf.VcfEntry.parse(VcfEntry.java:1012)
at org.snpeff.vcf.VcfEntry.<init>(VcfEntry.java:247)
at org.snpeff.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:131)
... 9 more |